two typefaces installed in font family, but no option to choose from the two.

Are these the Adobe, or Linotype versions? Also, Type 1 PostScript or OpenType?

That shouldn't be a problem as they won't have any conflicting names between each other, and OS X doesn't come with any versions of Franklin Gothic, though MS Office 2008 and 2011 do.

Testing with the various versions I have, the older Type 1 PostScript version of this typeface does conflict with the Office 2011 font (regular face). So it's possible you have a font conflict, though Font Book should warn you of that.

You could try resetting Font Book. Not always the reason, but a damaged FB database causes problems like this. Such as fonts you are told are active don't show up in all apps, or any of them.

Close all running apps. Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point.

OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.

Okay, no help on the reset, but that isn't a "sure thing" approach. Works about half the time.

What you saw in Safe Mode is what should happen. Only critical system files are allowed to load. So that also means only a handful of necessary fonts.

If you don't mind, I'd like to take a look at the fonts. I know you paid for them, but you'll just have to believe I won't keep them. I already have thousands of purchased fonts, of which are three different collections of Franklin Gothic.

Please email them to retoucher at jklstudios dot com.