Safe mode boots fine but no normal boot

[TierOneTech]

I have a MAC desktop with El Capitan installed that belongs to a friend. When I first looked at it, the computer would take about 10 minutes before it would start to go to the desktop. That would take at least 5 more minutes before it loaded. If I tried to use finder, the unit would stop responding and finder would be listed as not responding. I then followed instructions to delete the finder plist file. I also went to look at the StartUpItems folder, but can not find one in the Library folder

I found 3 extensions in Safari (2 maps galaxie and one unknown) and removed them. This is all of the issues I can find at this time.

The unit boots into safe mode with no issues. I have run CCleaner for MAC and removed clutter. There is almost 900 GB free on the terrabyte drive. I ran the disk analyzer and it found no issues. I am stuck.

One final note, the owner has no idea where she put whatever disks came with the computer, so I lose a few options there!

Anyone have any suggestions?

 

[TierOneTech]

I also checked permissions in CCleaner and fixed a number of of them that were incorrect. A number of folders had ACL's. I accessed the start up folder through CCleaner. I disabled Intego and Affinegy and others. All that is left enabled is com.akamai.single-user-client and Intego Common. I can not disable either one. It still will not go past the white screen with gray Apple logo. Anyone have any suggestions?

 

[CoastalOR]

So you can only startup in Safe mode at this time?
Usually Safe mode working and not the normal User account startup means a problem with something loading in the User account that would be disabled during the startup in Safe mode.

Try creating a new User account and try a to start up with it or log in to new User account. What happens?

Have you tried starting in Recovery?

BTW, what model "MAC" are you using?

 

[TierOneTech]

It is a 21.5" All in One desktop, with an I-5, 8GB RAM and a Terrabyte drive running 10.9.5.
The owner is a friend of mine who is scared to death of breaking the thing. She called the Apple store and they were talking several hundreds to repair it so I volunteered. So now I am learning!
I added a new user and turned off the auto log on, it does not change, the unit only goes to teh white screen with gray apple and stops. It does not bring up the user screen.

 

[JohnDS]

Reboot while holding down Command-R to boot into recovery mode. Then go to the utilities menu and run Repair Disk. Make a note as to whether it shows anything as having been repaired. Then try restarting normally.

 

[TierOneTech]

I did that already. It found a series of files with incorrect file permissions and a lot of "unexpected ACL's". It fixed what it could but I do not believe that it removed the ACL's. Restart afterwards has no change.
Also, it is now struggling to get into safe mode. Wish I had a HDD health check as it is acting like it has failing sectors.

 

[JohnDS]

Run Repair DISK, not repair PERMISSIONS.

 

[Gregg2]

I also went to look at the StartUpItems folder, but can not find one in the Library Folder.

There is no "the Library folder". There are 3 Library folders. The StartUpItems folder is in HD/System/Library. But why not open System Preferences>Accounts to look at StartUp Items?

 

[Weaselboy]

Also, it is now struggling to get into safe mode. Wish I had a HDD health check as it is acting like it has failing sectors.

Do a command-r boot to recovery and use Disk Utility to run a verify disk. Does that report disk errors? If so, make sure you have a full backup before you run repair disk as that can cause data loss.

So where do we stand now with a safe mode boot? What do you mean by struggling in safe mode?

If it works in safe mode and not otherwise, that points to a launch or startup item causing a conflict since safe mode bypasses those items.

Look in the following locations for launch/startup items. The ~ is the current user folder.

~/Library/LaunchAgents
/Library/LaunchAgents
/Library/LaunchDaemons
/Library/StartupItems

If you want, you can download and run the app Etrecheck. That will create an anonymized report showing everything running. You can post that report here for us to have a look if you want.

 

[JohnDS]

@Weaselboy - the option to Verify Disk is no longer available in the El Capitan version of Disk Utility. Only Repair Disk. I agree that booting only into safe mode indicates problems with a start up item, but OP now says that he is having problems even booting into safe mode, which suggests disk drive corruption or a corrupted system file.

I suggested a couple of days ago that he run Repair Disk, but it sounds like he ran Repair Permissions instead. This seems strange as Repair Permissions is not available in El Capitan any more either, so perhaps OP is not running El Capitan.

 

[CoastalOR]

@Weaselboy - the option to Verify Disk is no longer available in the El Capitan version of Disk Utility. Only Repair Disk. I agree that booting only into safe mode indicates problems with a start up item, but OP now says that he is having problems even booting into safe mode, which suggests disk drive corruption or a corrupted system file.

I suggested a couple of days ago that he run Repair Disk, but it sounds like he ran Repair Permissions instead. This seems strange as Repair Permissions is not available in El Capitan any more either, so perhaps OP is not running El Capitan.

In Post #1 the OP said the OS was El Capitan, but in Post #4 the OP said OS 10.9.5. I'm guessing since Permissions were repaired that it is, in fact, 10.9.5.

Anyone have any suggestions?

If you have the resources, it would be great if you could install the OS on an external drive and boot from the external to see if it boots normally. If the external drive booting has problems then you may be looking at hardware problems.

If the external drive boot is not an option then I would recommend backup, if not done already, and reinstall the OS.

 

[Weaselboy]

@Weaselboy - the option to Verify Disk is no longer available in the El Capitan version of Disk Utility. Only Repair Disk. I agree that booting only into safe mode indicates problems with a start up item, but OP now says that he is having problems even booting into safe mode, which suggests disk drive corruption or a corrupted system file.

I suggested a couple of days ago that he run Repair Disk, but it sounds like he ran Repair Permissions instead. This seems strange as Repair Permissions is not available in El Capitan any more either, so perhaps OP is not running El Capitan.

Understood... but OP mentioned 10.9.5 which would still have verify.

 

[JohnDS]

@Weaselboy - I suspect you are right and the OP is running 10.9.5.

If that is the case, he should also use Disk Utility to check the S.M.A.R.T. status of the drive. If it shows anything but "verified", then the drive is failing and needs to be replaced.

 

[TierOneTech]

I apologize for the incorrect statement concerning El Capitan. I saw that stated somewhere as I was first checking the system out. I then posted the 10.9.5 as that is what is what it is actually running.
I first accessed the disk check through CCleaner for Mac. It had a verify and a repair, which I ran both.
I then found how to access through the recovery and ran the repair there. It had about the same results as through CCleaner, less files with bad permissions, lots of files with an unexpected ACL connected.

Twice I had problems getting it to boot clean into safe mode, no desktop and extremely slow. Then it booted clean. I tried to check for start up issues but could not identify anything that looked out of place.
The EU called me and then I found out that she had an external drive connected and it was running Time Machine, so I am currently restoring a back up from before she had an issue. I will find out if it works!

Thank you to all of you for your time and help!

 

[JohnDS]

If you are getting messages about bad permissions or ACL errors, you are running REPAIR PERMISSIONS. You need to run REPAIR DISK. That is something entirely different.

Repair permissions simply repairs permissions on certain files. 99% of the time repair the permissions makes no discernible difference. Repair DISK repairs a damaged disk directory, which, from the sounds of our symptoms you have.

Boot back into recovery mode by holding down Command-R. The go to disk utility. Look at the bottom right of the disk utility window and see if there is a line that says "S.M.A.R.T. status". That checks the physical integrity of your drive. If it does not say "verified", you have a failing hard drive that needs replacing.

If it says "verified", go ahead and run REPAIR DISK (NOT REPAIR PERMISSIONS).

 

[TierOneTech]

The recovery has made things worse. Now the unit starts, brings up the white screen with the Apple logo, and then shuts off.
I ran both verify disk and verify disk permissions. Verify disk reported the disk was OK. Verify disk permissions found a number of issues. I have just run bath again, to the same results.
Weaselboy, does Etrecheck give correct results in safe mode?

 

[Weaselboy]

The recovery has made things worse. Now the unit starts, brings up the white screen with the Apple logo, and then shuts off.
I ran both verify disk and verify disk permissions. Verify disk reported the disk was OK. Verify disk permissions found a number of issues. I have just run bath again, to the same results.
Weaselboy, does Etrecheck give correct results in safe mode?

No it does not. Safe mode stops all launch items, so they won't be seen by the report. We want to see what is running during a normal boot.

From your description here, I am starting to think you have a failing hard drive. Confirm it still does not boot properly even in safe mode now?

 

[TierOneTech]

After booting into safe mode 3 times, now the unit goes about 1/3 of the way and shuts down.
I am now trying to reinstall the Mavericks OS from Apple.

 

[Weaselboy]

After booting into safe mode 3 times, now the unit goes about 1/3 of the way and shuts down.
I am now trying to reinstall the Mavericks OS from Apple.

I would not do that. If you do have a failing drive, reinstalling the OS really thrashes a drive and may push it over the edge. Reinstalling the OS is not the answer here.

 

[TierOneTech]

The verify drive test never returned any errors or warnings. The unit worked fine in safe mode, no hang ups or slow responses, until it would not boot anymore. I did the "reinstall" as prompted. Very different than Windows! Unit is up and running, installed updates, is now running Time Machine to create a new, fresh back up.
I did run the verify permissions for a comparison to the previous condition. There were no permission errors and no ACL's found where there should not have been an ACL. I wonder how much they affected the system!

 

[TierOneTech]

Here is another question. As I was rebooting after some updates were installed, I saw the Safari icon bouncing. I went to click on it, but it never opened. I had to go to the force quit to close it, where it said it was not responding. I did notice that there had been a MapsGalaxie toolbar and extension, but I thought I had gotten rid of it. Now Safari will not open, the error that it wants to send to Apple just says that it hangs. Any thoughts?

Thank you!
[doublepost=1453189652][/doublepost]Safari issue fixed, not sure exactly what, but it is working. I downloaded Malwarebytes for Mac and ran it. It did not find anything it did not like, but it did trigger the AV to find 2 instances of a plist file connected to the MapsGalaxie MyWay toolbar, so I quarantined them, after that, it worked. I was able to get into Safari and remove the MapsGalaxie extension. I had previously run a system scan with the AV but it had not found anything. Now it did. Weird!

 

[TierOneTech]

I thank all of you for your input! I appreciate it very much!