Yeah, I'm thinking ROM Manager did something hinky... It told me that there was an update to CWM, and without looking closely I said to go ahead and "flash the new ClockWorkMod Recovery." Only after I did that did I notice it flashed an OLDER version of CWM (I had the new Version 3, and it flashed the older version 2). That might be what did it.
You mentioned you had a problem moving an APP to SD... I noticed Sapphire and Sourcery have a problem moving APPS to SD the first time with a "Failed to move App" but if you try again right after that it works...
But yea... I think running fix permissions during a fresh ROM boot might have mucked something up, it's sort of a fragile state to be performing high level system commands.