I think i figured it out, and yes, you are right about the checked items. But there were more unchecked entries in msconfig than in that reg folder. However, i found the missing ones in the folder that the startupreg folder is in called "startupfolder". In other words, the startupreg folder is a subfolder to that one and the missing entries are in that. Why, i don't know. And i will export them before i delete them just to be safe.
I would use that cc cleaner, but i hate installing yet another app just to do one thing lie this.