It's possible that you're seeing an artifact of the 3.0 alpha firmware. I seem to recall that there were a couple of minor bugs related to marking tracks that got fixed very close to the end of the 2.0 product lifecycle, and I believe the 3.0 branch didn't get all of them rolled in.

The bug, if I'm recalling correctly, had to do with the very last marked track not properly getting unmarked if you tried to unmark it with emplode. Or something like that.