First, repair permissions: apps/utilities/disk utility/repair permissions.
If that doesn't work then get the free Linotype FontExplorer: http://www.linotype/fontexplorer. Run it. Then got to Tools/Clean System Fonts Folder. Those fonts are moved to a folder in your hard drive, labeled in all caps. Move those and all your other user fonts (no system required) to a folder in the first level of your hard drive.
Open FontBook and turn off all fonts it has activated. Turn it off and never use it again.
Go to FE and Add to Library to add that fonts folder you created with your fonts and the moved system fonts. Activate the fonts you want, just don't activate Times.