is it MS1(eek) MS2 or MS3?
are you triggering on leading or falling edge?
i doubt dwell is the issue, simple things first; how free from noise are the VR signal(s) at the megasquirt-end of the loom?
for the VR signal, i'd use twisted-pair at the least or preferably a fully shielded cable.
you might need a 'scope, setting my VR zero-crossing (R56) and hysteresis (R52) on my jimstim helped but on the vehicle it could be different. i made a crappy youtube video a while ago, which might help -
also, be sure you understand this document
http://www.megamanual.com/ms2/vradjust.htm
EDIT: could you drop your msq and a datalog here also?