The Uninstaller Tool ran smooth and did the cleanup without any problems. I used it to cleanup after uninstalling Comodo Firewall 5.3 on Windows 7 Ultimate. As I mentioned before for some reason I had a problem installing the newer version (5.4) over the existing installation (5.3). Even after uninstalling 5.3 I was still unable to install 5.4. After running this app I was able to install the newer version without any problems.
When the UT 0.3b was cleaning there were a lot of "can't find or failed to find entry/file...?" or something similar in the scrolling text in CMD window (the text was scrolling pretty fast). I guess that's due to the fact that the Comodo's built-in uninstaller had already removed those entries/files. And also because I had only the firewall portion installed and not the entire CIS suite. Either way UT was looking for entries/files that were already removed or didn't exist from the beginning that's why I think it was reporting that it couldn't find this and that. Of course that would mean that this is not a problem with the app.
Since you say first to use the Comodo's built-in uninstaller and then this little app perhaps it would be more appropriate to name it "Comodo Products Cleanup Tool" instead of "Uninstaller Tool"? Although it can be used as an uninstaller its primary function is cleanup, right? Not to mention that the name "Uninstaller Tool" is kinda vague.
Another small suggestion would be an after-cleanup log in a txt format. Since this is a portable app this log would have to be generated in the apps current/active folder. A message at the end of cleanup would indicate were the log.txt was created. Or, since you already have a message at the end of the cleanup "this windows will close in 10 seconds", you could have a popup message after the CMD window closes giving the user the option to open the log.txt file. There are people that like to see what exactly was deleted/removed during a cleanup.
I have no other suggestions/observations. The UI is clean and functional and it looks like this little app does what it was designed to do. Nice work.