I've been having a go with the 29994 file you produced above Ray. I have been using a UKTivo 2.5.5 for this as I can change codes etc without going into GS etc.
I have found that the codes select correct channels every time if I set the Tivo for no padded digits ie tivo only sends channel number with no 0 or 00 before. ie. TV1 = 1 only sent not 001.
This is not an option in the 3.0 US image.

I have also had a brief try at capturing codes as you did on the UK Tivo but found the no directory problem - the fix is further down the Use the OzTiVo to Capture IR Remote Codes With the IrSliceCreator Program page. I did get the program to work but haven't managed to get any results.

I will try the UK Tivo to record Sky next week and report back.