Do those learned signals work? They don't look like good learns, so I wouldn't expect them to work.

Most IR controlled A/C systems use signals that are too long for a Pronto to learn. But I would expect slightly better results than those.

The second learn looks like the original remote started to send before the Pronto started to learn, so the beginning is missing. That should be easy to fix when relearning. The first one looks like the Pronto saw a repeat pattern that wasn't really there and that made it learn incorrectly. That's much harder to deal with. Probably you would need information from learns of other functions to deduce what On/Off should have looked like.

How many functions does the original remote have? With problem signals, it helps to examine a bunch of different functions.

Does the original remote remember the device state? In many A/C systems, the remote remembers the state and sends full state information for each command. So there wouldn't really be an IR signal for TEMP DOWN. Instead, the remote would remember the previous temperature. The TEMP DOWN button would lower the remembered termperature inside the remote, then send a disrete temperature command for the new temperature.