Most images work pretty well these days - hopefully you'll be back to normal speeds and operations fairly soon.
I too have noticed more and more issues with file permissions in the last week, most related to Windows 8 apps, or to the 8.1 upgrade. I haven't seen this before from a major update, things are usually tested out very thoroughly before release. I'm a little at a loss to understand Microsoft's tossing and pitching about - they've been making some strange decisions lately, whereas had they just stuck to their historical posture of flexibility & wide choices for their customers, they'd be in great shape. [There's no reason they couldn't have provided the ability to switch between the standard desktop (with Start Menu & windowing) and the touch-oriented Start-Screen interface --- really: Ubuntu allows users to switch between these two styles with a single click].
I'm going to test the 8.1 update this weekend. I've been telling my customers to wait a week or two, and see if any major errors pop up (& get fixed) -- and until after I give it a thorough test myself. As the famous Dr. Who says, then it's "Geronimo!".
Best of luck
. . . Gary