Timing factors running through the computer interface/software can mess up the codes. Doesn't always happen, but enough times to make it unreliable. The more processes the code travels through to get to the IR window in the software, the greater the chance it's no longer clean.

As far as your code goes, make sure the batteries are fresh/charged in BOTH remotes. You could also try the files area. Short of that, post a new thread and ask for the codes.