It sounds like you have it set to pulse two times to lock the doors, but your saying they do lock witch has me wondering also.
I have seen similar issues on GM cars and the wires that were taped into where the problem, so I'd suggest re-checking them first. I have often found the same wires code's coming from the car but having two sets of wires inside the car. Make sure if the data module has settings that they are RESET, witch may require a power cycle of the module.