Are you getting nothing on the Repeat output then?
The LEDs are controlled by independent MCU pins so the reverse LED should not have any effect on the rest of the circuit. And the transistors are pretty hardy, so if it is in the right way then it should be okay.
Have you got a scope or multimeter to check the signals on the board?
I would have a look at REPOUT coming from the MCU (measure at MCU pin 16), make sure there is activity there when the module is on and you are feeding a clock into MULIN.
And check R701, R702, R703, R704.
Failing that maybe Thonk can give better support, they do the kits for us!