Very interesting Paul!
I want to book three weeks this year and have had exactly the same problem booking independently 'flight only' from Cardiff. I do from time to time get 'glitches' in the system, which will not allow me to book a 'single' seat, saying 'no seats available for these dates', but will allow me to book two seats on the same flight! Thought I was going nuts when 21 days were 'refused' on all flights and dates! So I think it's not the accommodation that is the 'spanner in the works' but the aircraft seat booking arrangements, assuming 'most' people want one or two weeks holiday, not three.
My local Thomson travel shop is only just round the corner from where I live and the staff are great. The only problem I can foresee if I book at the shop, is the 'booking fee' of around £30 which is not charged when booking 'on the net'.
Another interesting point is that Thomson are now not doing in flight meals on journeys under four hours. Instead, they are doing 'in flight snacks', jumbo sausage rolls, burgers, soup etc. a bit like 'MacDonalds in flight', not impressed.
Let me know if you get any 'joy' re. the booking problem,
Good luck,
Martin.