On our second robot we have a pair oh shooter wheels drive by a mini cim. Our desired speed on it is around 3600 rpm. Currently our main robot can reach this speed easily, but on our practice bot the motor fails to get up to speed even with noticeably less friction than our original shooter. It also tends to stall out more and slow down under the load of the ball. Is there any electrical problems that could be causing this or would it likely be mechanical issues.
You should check these electrical items:
- Calibration of speed control if they are PWM.
- Longer wires could add electrical resistance to both/either side of the speed control.
- Wrong gauge of wire could be an issue.
- Bad auto-resetting circuit breaker in PDP should be worth a quick check.
- Bad connection somewhere.
- Check any feedback sensors if using a PID loop in the control system.
On programming check:
- The values sent to the speed control.
- If you are using PID loop check that the P, I and D are set the same.
Adds to my big-bag-of-CSA stuff 
Have you calibrated your motor controller? I’ve definitely seen behaviors where one direction on the motor controller seems sluggish because the signal is only telling it to go to something like 50% Vbus in one direction, rather than 100%
Measure the voltage being supplied to the shooter motor on your main robot when the shooter is going 3600rpm.
Measure the voltage being supplied to the shooter motor on your second robot when you are trying to make the shooter go 3600rpm.
Post results here.
Is the pinch on the ball any different on the second robot?
(compression)