Slow flashing red indicates one of the following fault conditions:
- Power supply under-voltage
- Over temperature
- Over current
- Limit switch activated in the current direction of motion
also,
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When a fault condition occurs, the motor shuts down and the LED indicates a fault state during the fault condition and for 3 seconds after the fault cause is cleared (except for the limit switch fault, which is cleared instantly). A slow flashing Yellow LED indicates that the MDL-BDC24 is not receiving a valid control signal.
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this is available on the getting started guide posted here:
http://www.luminarymicro.com/jaguar
So, lets walk through it... you replaced the battery with a known good one, so it's likely not under-voltage. You said it usually happens after a short period of driving, which makes me guess it's not over temperature.
Can you check the limit switch jumpers? Is it possible one of them is loose, and jarring the robot in that direction is causing it to slip out of place? i figure this is probably unlikely, but you never know...
That leaves us with over current. Switching directions from full forward to full reverse (or full reverse to full forward) makes your drive train have to work incredibly hard - you have a lot of mass moving in one direction, and now your trying to pull it in the opposite direction. If you have high traction wheels, or some slop in your drive train, this can cause the motors to stall -
pulling up to 133A for a CIM motor. I would take a close look at your drive train and ensure there's no slop or any way for the motor to stall on that side. Depending on your drive train setup, it may only be binding in one direction, which is why you can go fwd-rev just fine, but rev-fwd is a problem.