Try the short button presses first via re-learn. If we still get FFFF codes, we may want to resort to another option.
Do you have access to a OneForAll remote? If so, set it up and test with the IRLinc as mentioned on Page 12 of the manual.[Link: cache-m2.smarthome.com]
If that works, then we should be able to learn the codes into the Pronto as is supposed to be NEC protocol.