Stuart is 100% right. Code cleaning works under the "profiles" principle. You have to create a new custom profile in order to be able to change what cleaning options. Each profile can have different subset of all code cleaning options to be executed.
This is a new feature that we introduced in our latest release and some small problems can be expected (like the one Stuart points out). We are already working on polishing and improving this for the next release.
the Telerik team