^Nero Vision should be able to do this, yes.
I've only heard of WinTV in relation to the Hauppauge capture cards, and most of them have hardware mpeg2 encoders. Are your files in mpeg2 then?
I use a commercial product called VideoReDo to work with mpeg2, and the Womble programs are also good since both can do frame accurate cuts in mpeg2 with minimal reencoding. Womble MPEG Video Wizard DVD would fit your needs very nicely I think, and there is a free, fully functional 30 day trial to test it.