One possibility is that emplode cannot perform the fsck, but does not crash and continues with the sync. This can happen when there is not enough memory for the fsck to run (or complete). Remember that during a sync, the player application is still running, so there is even less memory to play with. So if you are running an alpha (larger memory footprint), have large drives (larger memory requirements to fsck), have third party applications resident (more applications in memory), this kind of thing can happen.

A manual check will clear the immediate need, and the hijack setting will eliminate it in the future.