SO while late to this thread, I wanted to add my fix (albeit I'm hoping it continues). After finding this issue on a few different discussions, and dealing with this for almost 2 days and many AppleCare calls, I completely on accident stumbled onto a solution (at least for whatever caused this on my OS). I have a brand new iMac Retina with Yosemite and realized that after a day that almost none of my PDFs or JPG files would open (desktop or external drive). Got the error of "do not have permission to view this file" yadda yadda (same as everyone else on this thread) and it only seemed to reoccur after about a minute every time I reboot. During this minute I was able to open previously denied files in Preview, no problem. Then suddenly, JPGs and PDFs denied me permissions, except the previously opened files, which remained accessible. Then I'd reboot and for another minute or so--I could open more files, until Groundhog Day started again. So, after trying to unlock, already unlocked files and repair disk permissions in disk utility, I finally rebooted for the umpteenth time and the reboot froze....progress bar stopped half way. 3 times. So now, I'm thinking---how great is this Yosemite OS and my 5 thousand dollar investment! I decided my only go to was to boot up in Safe Mode, which was begrudgingly slower than any Safe Mode experience I'd ever had on any Mac. But I went into Disk Utility and Verified Permissions, Verify Disk and Repair Disk Permissions. Then I Shut Down and restarted again. Voila! It not only booted up in a flash, but to my surprise, none of my files were denying me access. As I type this it's been 2 hours and everything is still working, like a new Mac should. Not certain how the same Repair Permissions in Safe Mode fixed this issue. So, as much as I can't guarantee this as a fix, I'd think trying it can't harm the OS anymore than it's glitch already has the user.