Moving this post to a new topic.
You may want to try tuning comskip to create a custom ini file for your conversion task. The link above tell you how to create a custom ini for comskip.
Specifically using the comskip ini editor, under Global removes → aways_keep_first_seconds is the parameter you want to tweak. This will tell comskip to skip the first X seconds of your show so you don’t run into this issue.
Here’s where you can find it.
Regarding the issue with the reboot/restart, it sounds like a issue with the windows services. I would recommend starting a new topic to discuss that separately.