I don't know much about Tetrix motors or DC motors in general, but from experience, physics, and a little bit of research it seems like these fluctuations would be caused by the voltage of the battery. Applying max current for a set time will cause a different amount of rotations based upon the voltage of the battery.
You can see this by just driving the robot around for a while, if you let the battery voltage drop enough you'll notice that the robot feels more "sluggish." A little bit of research on wikipedia and other sites will also provide you with quotations like "Generally, the rotational speed of a DC motor is proportional to the voltage applied to it."
Since the fluctuations appear to be affecting your autonomous I would suggest trying something like
PID to control your drive. You already have an encoder so if you have a little bit of time you should be able to get this going. If you need help getting a PID or any other system going feel free to PM me.