Have you been able to test the voltage of your battery pack? (You'll need a DIGITAL multimeter for this).
It sounds like the controller is kicking in its protocol for what it thinks is a low battery level. What you describe is exactly what happens when the battery pack is depleted. The controller shuts down the motor to prevent damage to the pack (by over-discharge), and also for its own self preservation.
What are you using for a power source? What batteries, and what capacity? If your batteries test fine individually, it might be that your charger is cutting out prematurely and not bringing the pack to full potential. The chargers that ship with the GM kit are dodgy, at best.
It would be interesting to know what voltage you read when the system is exhibiting this behaviour. If the reading you get is still within a reasonable range for the battery pack being used, it might be that your controller has poor tolerance components and is shutting you down prematurely. They use fixed components for this (no trim pots to precisely dial in the shut-off).
