Well, how odd. I woke up my computer to find my iTunes behaving in the same manner...
Well as far as I can tell Up Next is not "playing" well with Crossfade (pun intended)
To put it simply, with iTunes 11, you can have either one or the other. Not both. If you have Crossfade on, your play counts/dates will not be updated. If you don't, they will but you won't have any crossfading. I theorize that this new unnecessary feature has broke the functionality between Crossfading and the Last Played/Play Count fields.
Of course, what more can you expect from a powerful company like Apple? After all, Micro$oft Windows Media Player's crossfade has been broken for a while. Stupid software doesn't start timing the next song until AFTER the first one is finished, Someone sure as heck dropped the ball on that one. I guess it's too much to ask for everything to work as it should in either Media Player.