All right, well, just in case someone stumbles over this thread and wonders how I fixed the issue:
I moved to Dirmon2. At first I was concerned it wouldn't be able to have different profiles for different channels, but it can. You just create a default profile as a catch-all that just looks for wtv. Keep that one with no priority boost and tell it to ignore premium channels by putting something like _STRZ and then _SHO in the ignore section (I include the underscore so there is no mistaking it is matching the channel portion of the file name). Then create specialize profile for single channels (or multiple) and give them a priority boost of 20 or so.
When Dirmon2 does a double match on a file, the one with the highest priority will when and the other will fall off when it goes to run.
I have 3 types of profiles.
1, Default that catches anything
2. A profile that call Comskip with an ini that uses logos for determining commercials. This is used for 5 different channels for me. I use it when default doesn't work well.
3. Specific channel profiles that call comskip with special per-channel tuned ini.
Hope this helps anyone who stumbles over it. DVRMStoolbox served me well in the past, but it's much more complicated code than Dirmon2 and so it has more of a chance to break. Dirmon2 hasn't been updated since 2006, but as of today still works on Windows 8.1. I still greatly appreciate all the work and effort in DVRMSToolbox, and I still use DTBaddin (I've customized the code) for the actual commercial skipping,