Not sure this will be any help beyond letting you know you're not alone - well sort of not anyway.
I had, and I stress had, exactly this problem when I first went to v7. However it went away with v7.1 (and now 7.2). I've not since seen a font change to its faux bold (or whatever) variant.
And my situation was really only a simple thing - not as messy as yours sounds. Basically a file with, say, 75 helvetica neue bold as a sub head would change on next opening to 55 helvetica roman <bold>. A simple font replace would fix it of course, then I'd save, close, re-open and bingo back to the <bold> version even though no fonts had been activated or de-activated. Very weird. But like I said it went away in v7.1.
I use 6.52 (sadly) at work (my 7 copy is on my home kit) and I've never seen the problem, not once.
Here we use OS 10.4.9, Quark 6.52, Suitcase X1 at home I have 10.4.9 (previously on a G5, now on an Intel machine), Quark 7.2, FontAgent Pro.
Clearly there's something up, but I'm not convinced it's a Quark thing. I personally think Suitcase is history. Have you, by any chance, considered a change of font management software? Font Explorer is (I believe) free, FontAgent Pro isn't, but it is good.
Whatever you do I feel your pain mate, sounds nasty. Best of luck nailing it!
Greg
I think therefore I am, you're pink therefore you're spam