Learnt IR should be compatible. But I have heard that the UDB is not the same (the Pro's UDB is newer). I have changed a B&W (original Pronto) CCF into color and am using it on a Pro with no problem. There is also the fact that PE 1.05 is not compatible with the TSU-2000.
I taught the codes via a TSU2000.
assuming you mean that you used a TSU-2000 to learn the codes, my guess would be a bad learn. If you used PE to learn, then you should not. The Pronto is much better at that job then a PC