There is a way to make it so that emplode will not sync merely because the "time to sync" clock has expired. But if there is underlying trouble with the filesystems, this will not help you. The FAQ entry about fsck says a lot.

Given that you were just working on the player, I would recommend a full manual sync, just in case. This should reset all of the timers and fix any trouble that you might be having. For a "step by step" for a dual drive system, do the following:

q #quit the player application and go to shell
fsck -fay / #root filesystem first
fsck -fay /dev/hda4 #music partition drive 0
fsck -fay /dev/hdc4 #music partition drive 1
rom #read only music, just to be safe
ro #read only root, just to be safe
exit

Then try a reboot and resync.