I know this is an older post, but just to add to this ...
I am running a machine with Windows 7 Professional x64. Last night, Windows lost touch with my RAID controller from nowhere (I can’t say if the lack of a RAID controller or Windows was the reason, it’s not enough to view events). As soon as this happened, Tom disappeared from Windows Explorer (makes sense).
Then Windows pulled out a message in the system tray, telling me that I should back up my personal certificates (PFX file) somewhere, since I did not do this after a while. I ignored this step, since I never used anything that would require personal certificates (no EFS or anything like that), so I disconnected because everything was spinning at that moment (the page file is on the volume that goodbye)
After rebooting, my RAID array passed the test, so I booted into Windows and started working normally, and not in safe mode. Voila, everything is back to normal, or so I thought ... I am experiencing the same problem as here and published at http://www.dreamincode.net/forums/topic/277832-projects-became-encrypted-when -i-used-ext-drive-on-laptop-now-what / .
Thus, between these messages, we can deduce (possibly) that Windows is not doing very well with Removable Media or Volumes, which suddenly disappear without a clean teardown.
I’m not sure why this will cause our files to start using the Encrypted attribute for them, although this is still a mystery ... Unfortunately, I think we will simply be surprised, because this is probably the Windows hood in WinFS, HAL or one of these untouchable layers of abstraction.
I hope this additional understanding can help other people understand that the WTF is coming up with this.