Thanks both...

Daniel, that's what I did before writing... I'd been using some random BluRay codes, I just changed to using the Pioneer TV ones I'd mentioned in the original post. They are from the Pronto database, not learned, this is two different IR codes that behave the same.

I don't seem to be able to look at the hex for codes in the Database, am I missing something? Suppose I could teach it to another Pronto then look at it?

Could this behavior be related to an IR relay? There is a Xantech IR receiver, amplified connector block and flasher on the ATV... I will see if it still happens if I point the remote directly at the ATV. Seems odd it would affect only one code though.