The learned codes and the codes taken from the manual are both RECS80 IR protocol, and while the Pronto Hex looks different, they are actually very similar signals. As Lyndel has said, this is a toggle bit problem, rather than a mis-learned signal problem.

Regarding trying RC5, although Philips designed both RECS80 and RC5, the two protocols are very different, and I guess that the OP's equipment is unlikely to respond to 5000 style Pronto Hex.