Go to FontBook Preferences and try checking disable just the collection.
If you use Classic applciations, You're probably best off storing all fonts in System Folder (that exact name) so they'll be available to all apps.
If you're all OSX, then try putting all in Hard Drive/Library/Fonts.
Please be aware that you might have fonts stored in User/Library/Fonts, in a fonts folder associted with an application, So it might be a little hard to locate them all.
Also note that there are some fonts in System/Library/Fonts. Some of these are necessary for the proper operation of osx. Note these and make sure they're not duplicated in another fonts folder.