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You formatted your drive as case-sensitive, journaled.

best way to fix this issue is to reformat, re-install as journaled (non-case-sensitive).

you can try all day long to set hidden attributes, turn off invisible files, etc but it won't work.

and renaming them to .XXXX is not going to work either -- even if the system lets you, it will bork things.
 
I think you can go ahead and delete those alias folders. The original folders won't be deleted.

That's not an alias, it's a Symlink... I wouldn't go deleting them either. You're starting to mess with parts of the UNIX subsystem that you don't know anything about.

As for me, I'd recommend reinstalling.
 
I had this exact problem on my iMac about a year ago and started a thread. I got the answer. Install Developer Tools from your Install DVD and run the following in Terminal in Mac OS X (not the DVD). If this doesn't work (it was perfect for me), reinstall.

Code:
sudo /Developer/Tools/SetFile -a V /bin
sudo /Developer/Tools/Setfile -a V /cores
sudo /Developer/Tools/Setfile -P -a V /etc
sudo /Developer/Tools/Setfile -a V /mach_kernel
sudo /Developer/Tools/Setfile -a V /private
sudo /Developer/Tools/Setfile -a V /sbin
sudo /Developer/Tools/Setfile -a V /tmp
sudo /Developer/Tools/Setfile -a V /usr
sudo /Developer/Tools/Setfile -a V /Volumes
sudo /Developer/Tools/Setfile -P -a V /var

Then delete the files that start with /Library/Caches/com.apple.LaunchService. There should be two.

Then reboot and it should be perfect
 
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