Did you check the bottom of the channel list (the 800 nos.) for the missing set of channels?
When you run the set-up, the outcome reads "there are different regions available: select your preferred region from the list below"(Northern Ireland and RTE NL1) and you must pick one before it'll allow you to continue.
I can't see any way of getting round this. (As well as the stations I mentioned earlier, I also get RTEjr, 3e, and RTE News Now. All perfect pictures but...you see my dilemma?
Just checked there - the southern stations don't appear at the bottom of the British ones as 800 numbers.