I think perhaps your font menu in earlier versions of QuarkXPress was being modified by a third-party utility such as TypeTamer. I don't recall QuarkXPress ever sorting recently-used fonts at the top of the font list.
While TypeTamer went away with Mac OS 9, here is a solution that will do what you mentioned:
Unsanity's FontCard 1.5 ($17 shareware) adds this ability to all applications, and adds additional helpful features: each font in the list has an icon that indicates its format (PostScript, TrueType or OpenType); it groups font families into submenus; and you can create your own custom font sets in the font menu. It also groups recently used fonts in at the top of the menu, marks duplicate fonts, and lets you reveal the font file for any font in the menu.
more info:
http://www.unsanity.com
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