I get that too. Especally with Fruitiger & Zapf Dingbats. This happens when you have more than one family of fonts. For example I have the Frutiger d fonts, Fruitger Open Type Fonts, and POstscript fonts.
For some reason Quark does not like some d fonts & it has trouble with some open type fonts.. I think it is a bug in Quark because none of my other programs have this problem.
So I need to go into the Utlitlies menu & under fonts, manualy switch out the fonts Quark is having trouble with for another "brand"
Suitcase will automaically open the d font first, then the open type then the postscript fonts. Quark would prefer it the other way around... thats where the conflict with Suitcase comes in... QUark like the old fonts, Suitcase wants to activate the best working fonts.