My guess would be that your database is hosed. Try following the instructions to dlete the database found in this FAQ and then resync with emplode. You might also want to try JEmplode at this point (possibly after deleting the database again), as I seem to remember that it handles unknown file types a little better than emplode (but I might not be remembering correctly on this one).

Caveat lector: I've not done the database delete thing, and I don't quite remember if it has effects beyond simply cleaning out the database to be rebuilt. I don't think it does, but I could well be wrong.