Couldn’t really find anyone else having this problem. All my fonts are activated in Suitcase Fusion 4, however when I go online the fonts aren’t there on many sites, just boxes. I have “what the font” running on chrome so I know the fonts that are missing and it’s ones like Verdana and Helvetica Neue. It seems like it comes and goes. It’s VERY frustrating. I am running suitcase on OSX 10.7.5 if that makes a difference.
I’m assuming you still have the Apple supplied Helvetica Neue.dfont installed in your /System/Library/Fonts folder? Have you tried another web browser (e.g. Safari) when you hit the problem? Sounds more like a browser issue than a font issue. Suitcase can override System installed fonts, and maybe the browser just doesn’t like the alternative version you have active?
I seem to have fixed the problem. I found (from another source) someone suggesting to turn off all the fonts in suitcase that appear in the font library (/Library/Fonts). This seems to have fixed the problem.