Has the extruder stepper driver circuit failed in your RapMan or BFB 3000 controller board?
Here is how I fixed mine in about 20 minutes using only a single piece of wire!
The BFB board Version 3.3 Part #30003 is used in both the RapMan 3.1 and the BFB 3000. These boards have 3 Extruder outputs. That means your RapMan 3.1 has a built-in spare! Or TWO spares if you are running a single head. The trick is how to access those spares? While in theory it could be done in the firmware, I don't have the ability. So, I went for a hardware based solution. I began by tracing the circuits until I was able to identify the critical wires. It turns out that BFB made things exceptionally easy by sending all 3 extruders the same signals in parallel, and only making the "Enable" signals separate. That means that only one jumper is needed from the Enable #1 trace to the Enable #3 trace. The only other thing that is needed is to cut the traces leading TO stepper driver #1, and FROM the CPU to stepper driver #3. After that, just move the wires on the 25 pin connector from Stepper #1 to Stepper #3.
Update: When I did this repair, extruder mapping was not in the firmware version available at that time. Now it is, and that renders this fix obsolete. However, you may have to replace a driver chip someday, like I just did when I fried another one. The Allegro chips do not tolerate having their outputs grounded. Having learned from the first disaster, this time I used my milling machine to cut the body of the chip away, leaving just the pins. These were now easily removed one at a time with a small tip soldering iron. Mouser's catalog listed the Texas Instruments DRV 8811 as a direct replacement, with a disclaimer, of course. I looked at the pin arrangement, voltages, and everything looked good, so I bought some. I soldered one in by first putting a small blob of solder on the circuit board heat sink pad and then heating the board from the back. The chip nicely settled into place, and then I soldered the pins. Sure enough, the chip ran the extruder drive nicely. Interestingly, the motor is much quieter, for the TI chip runs at a lower PWM frequency. The motor also runs slightly cooler, but has the same torque as before. However, when I tried printing, something was wrong. Soon I realized that the stepper was running too fast. Twice as fast as it should. Then I remembered Mouser's disclaimer and went back over the data sheets for both the Allegro and TI chips. The Allegro offers full step, 1/2 step, 1/4 step and 1/16 step. The TI has full step, 1/2 step, 1/4 step and 1/8 step. The BFB board was set for 1/16, and the TI chip was running at 1/8, or twice as fast.
Wires from left to right: Ground, Clock input to flip flop, "Q" output from flip flop, and +3.3 volts.
This works perfectly. My two extruders now track perfectly in speed, with the only noticeable difference is that the motor being driven by the TI chip is quieter.