CCleaner finding too many registry items

Ive been using the registry cleaner for a few years and now its showing thousands of entries every time i scan, it even shows items that are no longer in the registry (couldnt find it in regedit) and entries to some programs i havent installed since my last reformat. I decided to delete one of the entries from a program i didnt have (after makiing a backup) and my computer started to have trouble loading windows, So i restored the backup and tried again with a entry that did exist with the same results, Spybot and Malwarebytes didnt find any problems and im not sure what to do with it... I would like to be able to use it again since i usually get a noticible performance boost after cleaning the registry.

if it helps im running windows 7 ultimate 64bit, CCleaner v4.09.

Hello Twurtle - The only thing I can think of is that a previous version of the registry containing those extra entries was somehow restored. Have you used system restore recently, and if so, was it an old restore point and not a recent one?

I always use recent restore points, and last time i did it was after using the registry cleaner so yes it was recent.