Are you using backlash compensation in Mach3? are you using a counting board like smoothstepper? and one last question, is the drift in one or two axies?
all of the problems I had with Mach 3 and my conversion were attributable to windows counting ability. or perhaps more accurately its interruptibility. since I put on a smoothstepper, I have been able to run at full resolution and have had no more great lurching kachunks from windows getting distracted. I am not however running the dual dc drive.