So, I have "Use hijack" disabled, and I'm using the given command line to rebuild my player database, but all the playlists vanish. When I re-launch jEmplode, it forces a media check, and then reports "There isn't a file with FID 2 on this device."
Yes, I have a dual-drive Mk2a. =(
That is not going to be related to the bug I mentioned, but for what it is worth I had the same problem. Does the new on PC database rebuild work with version 2 of the player software?

-Mike
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EmpMenuX - ext3 filesystem - Empeg iTunes integration