We've often had this problem with the Humax 9200t freeview pvr and are currently experiencing problems with all BBC channels. We've been recording The Trip and Mad Men and lately the machine doesn't record for about 30 - 60 seconds at the beginning and end of the programmes, which is obviously very annoying. It's been going on for about 2 weeks now, I think.
We've always found the BBC channels to be the worst offenders, I'd always assumed this was because BBC programmes rarely if ever start and finish on time, but maybe it is something to do with the Humax.Padding a minute either way always sorts the problem, but it also means that you can't record a whole series with one press of the button, but have to record each show individually.I don't remember having the problem with any of the commercial channels as these are usually "padded" by the commercial breaks at either end.
We've also had problems with the Humax just not recording programmes at all, even when the record symbol is on the epg.This, I think, is a problem with the Humax and it usually requires rebooting the machine.
The Humax isn't perfect, but generally seems more reliable than many other makes and the picture and sound are fantastic, so we're prepared to put up with its faults and when we finally get freeview hd in this area I'd definitely be interested in another Humax.
Having said all that, the only advice I can offer is to try rebooting your machine and if that doesn't work try restoring it to default and then rebooting it. It's worked for me. Good luck.