I’ve been steadily upgrading with Extensis forever and am now using Fusion 5 for Mac with Maverick. I upgraded last December and everything worked fine.
As an example, using InDesign CC, I would select a folder in my Font Library that included 3 fonts. I’d have 3 fonts listed under “Type” in IDCC. As of today, I have way too many listed in there even though I have a single folder selected. I have no idea where they came from or how to get rid of them.
I “think” they might be Microsoft fonts that have somehow got in there when I had to update Word. They mostly seem to be True Type.