I tried MCE Buddy with Comskip but never got it to work successfully. :-(
I also tried copying my working Comskip ini file into the MCE buddy folder but that didn't help either.
One thought I have just had is that maybe the version of Comskip that is bundled with MCE Buddy is old or different? Maybe replacing all the Comskip files in MCE Buddy with a newer and known working version might fix it?
Cheers,
Nick Name