It is an MCE signal, so it almost certainly has a toggle bit. With or without a toggle bit, two learns of the same button are likely to look different enough that a non expert wouldn't be able to tell whether they are really the same.

I was trying to understand the symptom description well enough to guess whether a toggle bit problem could explain it. I can't understand well enough what was tested and observed, but it doesn't seem like a toggle bit problem would explain it.

The only symptom of a toggle bit problem should be that a learned signal won't work twice in a row. So you shouldn't be able to get play/pause to work again IR or RF after using it once, until you've used some other command. Once you've used any other command, play/pause should again work once IR or RF.

I don't see how that could make it seem that IR works and RF doesn't.