MMP-8 and Basic Atom

I have been using a 4WD2 to carry air sampling equipment. To upgrade the equipment I have moved over to an MMP-8 from the Machine Lab. I am running a Basic Atom 28 on a bot board II, my first bot used BA 28 and the mini board. I tried using the same code and the speed seems to vary from run to run. Clearly something is not resetting on their controller and I assume it has to do with the custom controller the MMP-8 uses. I have been in touch with their tech people on the dip switch settings. I can make it run at the desired speeds but when I try to input a complex program (which runs fine on the old bot) the motor speeds do not seem to correspond to the settings. Has anyone out there played around with the MMP-8 and can offer any suggestions.

Many Thanks!!