I think things seem to be going pretty well now.
I have replaced Showanalyzer completely with Comskip.
I have made the following changes to the default INI in the donator version with help from Erik:
shrink_logo=12 Not sure why this helps, but Erik recommended it
live_tv=1 for live tv
lowres=1 I tried lowres=2, for faster processing, but logos were being missed.
output_dvrmstb=1 for useage with dvrms toolbox
delete_logo_file=1 To get comskip to clean up
I also changed Verbose=0 for now, since I'm not testing.
I also have the following settings in DVRMSToolbox (dvrmstompegsettings) in filewatcher tab settings:
Wait Time=0
Poll time=30
In the DVRMSToolbox tab, I changed the Find Commercials in DVR-MS profile. I added a "Sleep for 5 minutes" task using Durrant.Plugins.Sleep, and added this to the top of the profile.
These settings cause DVRMStoolbox to wait 5 minutes after seeing the file before starting comskip. I found that if I just changed the wait time setting in filewatcher instead, that this means that DVRMSToolbox waits until the video file isn't changed for 5 minutes, which can cause compskip to not run at the correct time. I really wanted compskip to run 5 minutes after the first file write of the video.