I also have this issue - maybe it depends to the new window restore feature of Lion?
I didn't research a lot, but it seems I see this issue if I shut down my Mac while PM is running.
After that I've to use TimeMachine to restore Library/Preferences/*photomechanic* - timestamp a week ago
I'm using PM 468b1 on OS X 10.7
Sorry for less details - I've to develop images of a wedding this weekend