Mihaid, there is a hypothesis being postulated, based on your limited evidence, that ITV and Ch4 are not broadcasting the necessary information on their HD channels to allow correct operation of Accurate Recording.
Over the 2 years I have had an HDR-Fox and 2.5years I've had an HD-Fox I have only had Failed to Track messages a few times, all associated with the broadcasters moving programmes or, in one case, my scheduling of a series when one episode of a conflicting series recording was not being broadcast that week and thus the Humax could not spot an arising conflict.
If the problem was as widespread as you suggest, a lot more people would be up in arms.
I do not believe the customised software affects matters but I think you should reset your box completely, stay with the standard software, carry out a manual tune and then see whether your box still suffers the problems.
If you still get problems then I am willing to parallel some test recordings after 2300 (to avoid SWIMBO's recordings) to see if your box is faulty in some peculiar way or the broadcasters are at fault.
Martin