I don't want to change the file contents at all. I don't want to remove the commercials. I just want to generate the xml file for DTBaddin to use to skip commercials and move the file to a new location. In the log I posted below you will see that the file was remuxed to a TS then back to a wtv. This causes a ton of extra reading and writing from the disk, as I just want to use comskip to process the WTV file directly. I noticed in the expert settings for the profile in mcebuddy that I can select "skip remuxing files", but when I select it and click ok then come back into check that it was set it looks like it never stays selected. Not sure if that is a bug or what.
http://travisandliz.com/mcebuddy.log
http://travisandliz.com/mcebuddy.log