Odds are it has nothing to do with Jemplode.

It's probably the same thing I was running into: As soon as you move userland programs onto /drive0/, certain aspects of the synch start failing if you're running those apps in AC power mode.

The drive unmount/remount commands (used in a synch) quit working when an app is running off of that partition.

You need to make sure all your apps on /drive0/ are tagged as @DC only, and then only do synchs in AC mode. After you've done that, you need to do this to fix your drives. After that, you should (in theory) be OK.