Hi,
There is no problem with the install choice you made based on the SDK installation guide, as it is the least problematic of the pack (install as user + run as user = no problems with permissions) - the install choice I use is the worst case scenario (that is why I use it, to fool proof CCS in our internal testing and usability).
In this particular case I can't tell for sure why you are seeing this behavior. As I mentioned, try to open a new workspace and see if the settings are still "stuck". Another idea is to launch CCS with the -clean option (check these two tips and more in sections 3 and 4 here). Apart from this I am not 100% sure what else could be happening on your case, as I couldn't find any reported bugs about that.
I didn't realize you were the same person that talked about the \t. I will explain it at that thread so we don't lose the flow of information.
Regards,
Rafael