I see what you are trying to do now. For us, scripts are just part of the testing, but your process is a bit different.
My first suggestion would be to take some of the time that you are using trying to figure out this logging issue and working around it and fix the actual tests. I'm sure a lot of us feel like we never have enough time/resources to fix our tests, but I think this would save you time in the long run, even if you just fix the ones that cause you the most trouble.
We have "tests" that actually do setup as well. They're separate from the testing, so they don't end up in the same log. If you are running overnight tests, could you run the setup earlier in the day so it doesn't count against your testing? Or put it in a different project so that TestExecute looks at it separately and you could ignore those logs?
For your script that runs several tests, maybe this will help you pick the log apart to get the items you need:
http://support.smartbear.com/viewarticle/55140/
