Certain types of codes will not learn well through the software. In particular, codes that are converted to an internal database format seem to be trickier than those that are not.

For example, I have some Hitachi and Denon codes that, when I hold the source button down, the Pronto never seems to finish learning. After 5-10 seconds, the remote has basically locked up and I have to disconnect/reconnect it to the PC to continue learning. In these cases, just pressing the source button brielfly seems to work fine, and you likely notice the it ends up with a short 900A-type code.

Note that for all other types of codes (for example Sony) you *must* hold the button down until the remote finishes for a clean learn. And for yet other types, learning directly on the remote is better.