It sounds like the actual issue is unrelated to registering different colors. Here’s something to try: Run a short example file twice, drawing the exact same thing twice without moving the pen, and make sure that it retraces its steps well.
You haven’t hinted at what kind of machine you’re using here. If it’s an EggBot, please read through our quality troubleshooting guide: http://wiki.evilmadscientist.com/Eggbot_Quality_Troubleshooting
