This sounds like disk damage to the file tree structure. And it may not be limited to the Control Panels and Extensions folders. Run Disk First Aid (the verify command), see if it reports catalog errors, B-tree errors, missing file records, or volume bit map errors. There are others that could turn up as well.
If the errors do turn up, you will need TechTool Pro or DiskWarrior to fix it. Norton could probably do it also. Do not let DFA repair the damage, it would do so by eliminating the remaining parts of the missing file listings. Probably DFA will refuse to repair the damage actually.