Tivo have no idea why and have thrown random statements like I must be receiving them on my PC via the analouge transmission over 200km's away even though the aerial isn't even pointed that way. (typical response from an Australian based service support)
But today I think i've stumbled across the answer.
As I understand some channels transmitted from the Te Aroha transmitter (and possibly other transmitters around the country) sends a flag on certain channels that that channel isn't available in that particular area, and "Freeview approved receivers" take notice of this flag and block these channels, while the TV Tuner in the PC pays no attention what so ever.
But Tivo isn't a approved receiver, and looking at Freeview approval rules, Tivo will never become approved (due to the ability to transfer recording to another device). So if this is the case and Tivo's are following this flag, why are they? Why haven't they informed their customers? I does appear that they are blocking certain channels.
So if you think you are missing out on channels contact Tivo and put this question to them "Does Tivo follow the channel unavailable flag as brodacast by freeview?"