I found that with respect to cutting commercials out of H.264, so far, the only app I tried was video redo and it was always innacurate. It seemed to cut in the general area of the commercial block but there was no way it was frame accurate and this made it useless
When you explained it to me I did more research into it. I spoke with the creator of MC-TVconverter thinking he might be able to help. He mentioned much the same thing - that he was not aware of anything that would do frame-accurate cuts in H.264
I then spoke with Andy Van Til over at DVRMS-Toolbox and learned more yet but he mentioned much the same. He said it was too difficult an issue for him to tackle (not practicle)
At that point I then (you can guess I don't give up too easily!) found out about Smart Cutter, "The world's first H.264 AVCHD MPEG2 frame accurate cutter without re-encoding!" In fact, they actually say that it's perfect for cutting commercials out of files created by Hauppauge recordings (in H.264) which is exactly what I have....sounds perfect!
So...I asked a few questions in their forum to try to determine if the product was worth purchsing (for instance, can it make use of comskip commercials detection files so that I can automate the process) but they banned me from their forum due to their thinking I was a spammer! (they seem to have an unsecure forum that people hack and then hijack the accounts).
So.... it does look like there is frame-accurate cutting software out there, it's not too expensive, it has gone through a few years of revisions and bug-fixes (might even be mature) but they kicked me off their forum - go figure!
Update: I just looked into it again and downloaded their trial version (it's only 6 megs) but it seems that while it does support frame-accurate H.264 cutting it doesn't support the .wtv container that Windows Media Center records in. If it's not one thing, it's another!
I did send them an email though, maybe they will fix this. They should if they are aiming at the Haupaugge/HTPC/H.264 marketplace...