If the unit is indeed building the music databases, this can take a few minutes on a full unit: the fact it's building the databases means that the last sync didn't complete fully (the last stage of a sync is to rebuild the databases so they can be loaded quickly at powerup).
Try letting it finish at home on AC power, then run emplode and just click sync. If this doesn't help, mail
[email protected] - there may be something we can do (bugs have been found in the database code and we may be able to get you a fixed version that hasn't got released yet).
Hugo