MACPREPRESS  Getting a bit off-thread here, but I've seen this too. Several version 1.0 Postscript copies of Futura Condensed Bold wouldn't show in ID CS2. Then I found another "virgin" copy of the same font. All the rest of my current library has been through some combination of FontDoctor or Smasher. The "virgin" copy from 1989 worked fine.  
(Version 4.0.1)

MACPREPRESS  I was hoping that the 4.0 release would be better able to handle a couple things.

*lessen the font cache corruption issue

*be able to properly active the precise version of a font.

From what I tested, the caches degrade about the same as version 3.X, so no improvement there. I saw it get somewhat better at recognizing some fonts. But still it had problems with common ones like Zapf Dingbats.

Worse, after a bit of use, the plugin would crash InDesign.

I've been testing Suitcase Fusion 12.1.7, and it's not a bed of roses either. Auto-activation seems largely disfunctional. I haven't tried Fontexplorer yet, but I guess it's time.  
(Version 4.0)