I can’t reproduce the same bug that you have. I am using the black theme and everything is perfect. In fact I don’t see any relation in theme/protection.
what I think happened is he ran the test first, some rules got created automatically, he changed the skin and ran the test again. now because there are rules for the clt app, he thinks the skin change had something to do with it.
I also did what you have just to test that and I’ve changed theme to black and ran clt and i got 230/340 but when i returned to normal red theme score was 340/340.
I changed to “blue” skin last night, and after reboot, the whole thing went hare-wired! Defense+ started asking all kind of question again and I had no access to even my start menu! Eventually I have no choice but to restore from my backup… >:( >:( >:(