Another thing to look at is the finger spring that engages into the reel and keeps it from reversing. I've had reels that didn't score correctly and it was because that spring wasn't engaging correctly and when the reel went to step it would reverse slightly and usually come up one step short.
If the chimes aren't correct though I'd check the 100 point relay to make sure all the switches are right. The bane of EMs is switches that looking like they are making but aren't, and vice versa.