So after about a week of debugging this issue we've refined it down. When we run our motors, whether it be the drive through joystick or aux drive through button press, the motors will skip in phases. About 5 seconds of rough, 10 seconds smooth. The weird thing is that it's not dependent on the motors starting, its a constant phase changing. We can stop the motor in the smooth phase, then start and be smooth. Stop in the rough phase, start in rough.
I think it has something to do with our scheduler, but don't know enough about it to check if it's correct. Currently in Robot.java we have a Scheduler.getInstance().run(); in OperatorControl, disabledPeriodic and autonomousPeriodic. Can anyone help us with this issue?
BTW: This isn't a Watchdog issue. We've tried increasing the expiration on RobotDrive and it doesn't change anything.
Link to our code:
https://github.com/DeltaVii/1571-Stronghold