I’m using Sparks max with PWM for a drivetrain. When I go forward they all turn green, but when I go backwards they all turn different colors and starts to blink fastly.
Can you post a video of the LED sequence? It’s hard to guess what is happening based on your description.
What is the firmware version? There were a few fixes for PWM since the initial release.
We successfully used spark maxes with PWM in Java using the Spark class from WPILib.