Hey all, thanks to your posted comments, I realized that the exclusion list I posted here originally was not in the correct syntax for the InCtrl5 tool to understand it.
There is not a way to exclude files in the InCtrl5 tool, so you will need to look at the exclusion list at http://www.winisp.net/astebner/bin/inctrl5_exclusion.txt and manually exclude them after running the tool for the setup you are trying to model.
For registry keys, I have created a new file in the correct format at http://www.winisp.net/astebner/bin/inctrl5_registry.txt. You can download this file, rename it to InCtrl5.ini, and copy it to \Program Files\InCtrl5 on the machine that you have installed InCtrl5. This will cause the tool to ignore this set of registry keys/values when analyzing a setup.
Hope this helps....