I have almost the same problem with a Pronto NEO. The original firmware it had when I bought it would learn the IR codes from General Instruments digital cable box without much hassle (sometimes had to try twice to learn them, and it wouldn't learn one button for some reason). I then upgraded the NEO to the latest firmware (downloaded from remotecentral), and now it won't learn any of the buttons anymore on that particular remote. Still learns all my other remotes fine.

Weirdness.