Do you still have that old Pronto?
Some of the experiments that may be needed to solve this would be easier with an old (pre NG) Pronto. Other experiments need a second PC readable IR learning device (such as a second Pronto) in addition to the Pronto being tested.
I'm afraid I don't have an old (non NG) pronto, but I do have two NG colour Prontos.
If I understand you correctly, a short press always learns something but the learned command never works.
Yes, that's correct.
I see your ideas about capturing the end of the codes. I will try this and revert back. Unfortunately I'm still at work at it's 7.30pm so I don't think I'll have time for this tonight. I'll try tomorrow.