I have not tried to do it during the Database message, but I have tried during the loading playlists message and waiting the full 35-40 minutes till the player starts...no difference in symptoms.
It doesn't do a faster rebuild when all the var/* files are removed, and although it does eventually get to the player I can't play anything, and emplode fails.
Err.. missing step 0: kill off and close emplode/JEmplode *before* attempting any of this, and don't restart them until all of this has been completed.
Don't worry - I have only tried them once the player is running again.
I'll try the tunefs stuff though - see if it changes anything.