Manual commercial removal is EXTREMELY time consuming, and if that’s the route you choose, then that is what works best for you then. Since you messed around with the comskip settings, and possibly other settings with MCEBuddy, I would recommend that you do a complete uninstall of MCEBuddy altogether. Download that latest version, then reinstall and try using default settings again.
What program do you use to actually record your shows? Your recordings are OTA using an HDHomeRun Tuner, but curious what program actually records the shows for you? It can have a drastic impact on how MCEBuddy works I have found.