Check the Driver Station log to see if that sheds some light. Run the robot with the problem a few minutes, then look at the Driver Station Charts tab and in the lower right you'll see "Launch Viewer". You'll get a popup viewer with a list of logs by date to click on.
Driver Station Log File Viewer
Are the Driver Station Diagnostics or status lights showing any error messages?
I'd try the generic arcade drive, but with a different computer running the Driver Station. In case the computer is causing the pulsing action.