I don't have a solution but I've had a very similar problem with Inday codes and Crestron infrared codes. It only learns in the 2-learn command, but even then it's hit or miss. With the Inday codes, after over an hour of trial and error (and 'pulsing' the button on the remote to-be-learned) I eventually got all 4 of my buttons to work. With the Crestron codes they won't work at all, but I can learn them into an MX-850 and get them to work (strangely though I can't get them to repeat as they do on a Pronto).

Anyway, you have a kindred spirit out there. I still push the URC remotes at work (vs. Crestron and Pronto) but I'm leary of the day I find the one customer whose equipment I just won't be able to learn properly.

RobZ