I have been in contact with someone named Joe in Boxee support
I asked when they will have a fix for this problem. His response...
Joe, May 11 02:30 pm (EDT):
Until we can get a fix developed I recommend holding down the top power button until the box shuts off.
He then suggested the same old reset semi-solution [which hasn't worked for me yet]
Joe, May 11 10:35 am (EDT):
Sorry for the trouble. We are continuing to work on this problem. The steps below fix it in some cases.
Please power down Boxee, then press down the power button for 6-8 seconds and release (the Boxee icon on the box should turn to yellow/orange). You are now in recovery mode. Please select the "Reset All Settings" option.
Apparently, they're working on it, but he didn't offer any information on when they might have a fix...
This problem sucks. I am really worried about corrupting external media so now I just use my Boxee for Netflix...