EyeTV and Commercial Skipping using ETVcomskip - Mark commericals, don't delete them!

I learned how to add automatic commercial marking using essandess's excellent guide in this thread: EyeTV with Commercial Skipping HD DVR Server

However, I recently upgraded my hard drive and re-installed EyeTV (3.6.5) and copied over my ETVcomskip files from my old OSX installation. ETVcomskip on my old set-up used to just mark the commercials (rather than delete them) so I could use the advance button on the remote to skip the commercials using my Apple TV. This also had the side-effect that if comskip didn't quite get it right I could just manually find the commerical end/start. Now, however, my commericals are being deleting, and I'm missing chunks of shows (especially the part from the last commercial to the end of the show!).

Question: How do I stop ETVcomskip deleting commercials, and go back to the "mark commercials" behavior?

Thanks,

Ste