Whoop-dee-doo, i know the reason CLT behave oddly - sandboxing.
It's broken cuz sandboxed HIPS doesn't work for virtualizes files/registry - as obvious explanation, ....
We'll have to wait for more feedback from the developers. Apparently, it is much more complex than the explanations proposed by users and mods (and since we do not know the exact details of how CLT and CIS interact, we have to wait for the developers to provide more information). Currently, it appears that the CLT findings do not represent a bug in CIS, but rather a limitation in CLT. But, as I said, we have to wait for more feedback from the developers regarding issues such as:
1) Does a bug exist, and if so, is it in CIS or CLT.
2) Do default CIS and sandbox settings need to be changed.
3) Does CLT have to be updated to so that it can provide more accurate testing under any configuration.