I've seen that too, but I don't think it is an actual bug. Everything works fine if the registry contained nothing before, and it never happens again after you delete them, either.
It only seems to happen when you add one registry key to an existing set... no idea what's going on there, but it looks like Windows SNAFU.
There's another funny thing that can happen in that context, too. You can get two instances of Code::Blocks to continuously fight over who is the default application and end up having one file type open in one instance, and another in the other. I haven't figured how, when, and why that happens either. Actually it cannot happen...