Plex uses comskip for commercial removal, and you can customize comskip by providing a custom comskip.ini. (Scroll down to “Customizing How Commercials are Located and Removed”).
I’m reading that your HDHR prime outputs mpeg2 while I’m commercial skipping h.264, so I don’t have specific experience with your environment. A quick review of comskip available settings suggests that you may want to experiment with the settings for thread_count, hardware_decode (don’t know if you have or are using a GPU), and lowres (possibly lowres=10 for mpeg2 I read…)
This is also a good thread on custom comskip.ini settings.
