Hi Phill,
Sorry for the delay in responding. I'm very snowed under at the moment at work.
Could you post a couple of pictures of the soldered board (top/bottom) - I can have a look and see if there is anything I can spot that might be causing the issue.
If the motor is not properly moving in the way you describe, the issue is unlikely to be with the ATMega. It's more likely to be a bad connection between the motor driver and the motors - if one wire of the four is not well connected, the motor will typically just bounce around and make lots of unpleasant sounds.
You could check whether one of the contacts within the sockets for the motor driver is damaged, or if there is an issue with the RJ11 connector (e.g. bent/broken pin).
Kind Regards,
Tom.