Cutting off program just before commercial on FX, ABC Fam

[kyle]

I download shows off my HD TiVo, convert to mpg and run them through comskip.
I have seen that many times on shows from FX HD and ABC Family HD, it ends up chopping off some of the show just before a commercial. I tried tracking this down using the visual tool to review the markings. It looks like at some points it thinks the volume is zero, so it immediately marks it as a commercial--even though I still see the logo/red box on the screen. (I looked into this a month ago, so I don't remember all the details, but I believe the volume was getting counted against the logo, dropping that value.)
Is there a way to force comskip to never treat something with a logo on the screen as a commercial?

[erik]

That should be the default behavior, unless you changed specific settings to alter it
Maybe you can use the "how to ask for help" procedure to ask for tuning help?