I have the same issue as Randy. On my regular ipod it has never really been an issue because I rarely initialize and re-sync. On my Nano, however, I end having to close/re-open MC to give the correct space available for sync. Because the Nano is relatively small (1 GB version) I find that I am changing the playlists that I sync with quite often. Here is what I am doing:
1. Connect Nano
2. Go into options and change the playlists that I want to sync (I do have it set to delete files that are not in the current sync)
3. Recheck sync. If previous sync (files which should be deleted) and new sync combine to be more than 1GB, MC states that I am over capacity.
4. Initiallize IPOD. Recheck sync still incorrectly shows that I am over capacity.
5. Close/Re-open MC...space available now shows correctly.
6. Sync
I have kind of gotten used to closing and opening in order to sync so it is not a big deal to me. The only times that it has been frustrating are when I spend time manually dragging files over to the Nano only to find out that it thinks I am over capacity...Luckily, I have learned my lesson, and this has not happened for awhile.