JP1 Remotes

If you mean the RDF, you don't need to change it, the URC-9960B01 RDF will work fine with your remote, the problem is that IR isn't reading your EEPROM correctly. As you can see from the old posts in this thread, this has happened before and I thought it was fixed, but obviously UEI has used a different EEPROM in the URC-9966 than what has been used previously. So, the modification that's required is to the IR.exe program itself, and unfortunately, the author doesn't hang out here much anymore so I don't know what we can do to fix it.

IIRC, he did tell me that even when IR doesn't read the EEPROM correctly, it should still write to it OK. So you could try using the File > New > Select option and select the URC-9960B01 remote, then try loading it into the remote to see if it takes OK. This would let you add upgrades and do other programming using IR, bt you still wouldn't be able to download from the remote successfully, not without first un-wrapping the data, that is.

Can you confirm that, when you are doing a download using IR.exe, you have the "Force >=4k" option selected. If you haven't had this option selected, could you re-try with it selected.