There are a couple of things I'd suggest looking at first.
One is the Z-axis speed in your VCarve file. If it's set too fast the tool can "lose steps" and vary the cutting depth. There are also settings for the maximum move and jog speed in the FabMo Settings menu. Those are in inches/minute and I usually set them to something conservative like 120
I'd also check the file and make sure that it's not lifting way up and hitting the top stops when it lifts between parts. If it does that it will lose location and your cut will have wonky depths. Same if it hits the bottom stop when its cutting.