I did have to make some changes to some of the .ini and .bat files to get the whole comskip thing to work - it didn't work straight out of the box as it were. Comskip and comclean2 can be downloaded from here. Extract the files into your GBPVR directory. Cuttermaran can be downloaded from here. Extract the files to a temp directory and run the setup.exe file to install. Here's the changes I made:

1. Edited PostProcessing.bat in the GBPVR root directory to enable comskip and comclean2.bat - at the end of the file I think you have to un-comment the comskip line. Anyway, it looks like this at the end of the file, minus the comments:
comskip %1
:continue
call comclean2 %1
:eof

2. Edited comskip.ini file to enable creation of files needed by cuttermaran:
output_cuttermaran=1
output_demux=1

3. Edited comclean2.bat:
Rem bbdmux "%~dpn1.mpg" 0xe0 "%~dpn1.m2v"
Rem bbdmux "%~dpn1.mpg" 0xc0 "%~dpn1.mp2"
I remarked out these two lines because comskip demuxes the mpeg file when you set output_demux=1 as in step 2, so these two lines become redundant.
ren "%~dpn1_clean" *.m2v
This is the thing that drove me nuts - cuttermaran was creating a _clean file with no extension, but mplex1 expected a file ending with .m2v. It didn't help that mplex1 doesn't give any error message when it doesn't succeed in finding the file. This line renames the needed file with the appropriate .m2v file extension.
del "%~dpn1*.info"
del "%~dpn1*.txt"
del "%~dpn1.log"
del "%~dpn1.cpf"
There's a lot of useless files littering the directory when the process is done, I elected to delete them. If you don't mind the mess or you're debugging a problem, just leave these lines out.
if EXIST "%~dpn1_clean.mpg" del "%~dpn1.mpg"
if NOT EXIST "%~dpn1.mpg" move "%~dpn1_clean.mpg" "%~dpn1.mpg"
More cleanup, I delete the original file and leave the edited file with the original's name. I am risking getting stuck with a bad file if there's a problem with the editing process, but what the hell, I like to live dangerously. Plus, this leaves my directory with only one file, the edited mpeg of the recorded show. Nice and neat.

I think that's all I did. Hopefully this will help anyone having problems getting this thing to work. Oh yeah, in the GBPVR configuration program, under the processing tab, I have Commercial Detection set to None, I think that's just for using the comskip program during recording, the other way that I haven't tried yet.