If a track fails to make it to the player, it should still be marked as new or changed. Try doing an advanced search for: "new or changed" (minus the quotes), after the sync fails. If the tracks aren't in there, then you've found another bug.

The fact that emplode lets you add more tracks than it thinks you've got space for is by design. ISTR that it warns you when you press the sync button.

Theoretically, the free space indicator is accurate. Obviously, you've found a case where it's not. Unless you're running 1.03, in which case, all bets are off.