Wow, sorry I missed all of this. Based on all of the facts I am pretty confident we are looking at a PID setting issue.
Try decreasing Kp on the Velocity controller to 6 or maybe even 5. So enable custom settings for the velocity PID and the values should be
Kp = 6
Ki = 0
Kd =.28
I suspect the Kd will have to be adjusted if this helps.