Tony,

I would also suspect that Pronto has not seen sufficient actual IR code. As previously noted, Pronto does not confirm a code to be valid, simply that it has seen what woudl seem to be an IR code.
While I was teaching one of ny demo Prontos the Meridian codes, I found that some of the buttons registered in the PC software although I knew they were RC codes and therefore should have registered as . Upon relaerning teh codes with better alignment, they indeed registered as RC codes, as they should.
Unless the software when released includes "truth" table of some sort (unlikely) this only works for RC (Philips/Marantz)codes that are internal.
However, I hope this provides some indication about how noise and low ouput/misalignment can affect correct learning.