Security Update 2016-003 Problems with 4,1 MacPro

[fatespawn]

I came home the other day to a dark gray screen with only a cursor. I leave my Mac Pro on during the days so I figured it just had a hiccup and needed a reboot. After trying multiple times, I couldn't get past the startup progress bar. Apple logo shows fine, progress bar starts loading... then black/gray screen with only a cursor.

After multiple trouble shooting steps (First Aid, PRAM, SMC reset, Disk Warrior etc.) I just gave up and restored from my clone.

Anyway fast forward a couple of days and I noticed a "Security update" waiting for me (2016-003). I'm still running El Capitan. I clicked update, rebooted, and poof! Same symptoms. I suspect the first instance of the problem was the update too, but I never rebooted or noticed until I came home later that day. Frustrated, I researched the problem (now with a culprit in mind) and found someone with the IDENTICAL problem

4,1 MacPro flashed to 5,1
3.46 Westmere 6-core installed (mine is the W3690 vs. his dual processor X5690)

http://apple.stackexchange.com/questions/264863/security-update-2016-003-10-11-6-issues

Sounds like Apple bricked my pseudo-hackintosh. Has anyone else had this problem or found a workaround?

 

[carpsafari]

When you have the same experience as the one you quote, than you too have a corrupt home folder.

Try the guest account, no problems there? Than you are sure its your start-up boot.

 

[fatespawn]

Yes. First, I had Automatic login selected. Booting to safe mode, I managed to get my selectable user options. I was able to log into a "test administrator" account I have set up. That was seamless. Then I turned off auto-login and rebooted normally. However, rebooting into my primary user is still impossible. I enter the password, and get an endless spinning wheel. Interesting that the security update seems to affect only the account that was used to install the update. The alternate-admin account I have works fine.

 

[fatespawn]

Well, if anyone else runs into this problem, I unwittingly fixed my issue (more like work around). I had intended to stay away from this particular security update until I could find a solution, but much to my chagrin, I had previously selected "install security updated" in System Preferences/App Store enabled. So, guess what... AGAIN, I found my "update waiting for reboot" this morning. Yikes. Next reboot would likely brick my computer and require ANOTHER restore from my clone.

So, with no real option, I logged out of my primary user account, and logged into my alternate Admin account (the one that worked after the security update last time). I enabled automatic login for the Alternate Admin account and then installed the security update from THAT account. Rebooting actually went normally. Then I switched users into my primary Admin account and all seems well.

I really don't know what's going on under the hood with this updated, but If anyone else running a 4,1 machine flashed to 5,1 has this problem, you might try installing this security update from a new Admin account you create just for this purpose. Hope it helps someone.