Quark not seeing fonts in /System/Library/Fonts

I'm trying to rationalize some font setups, and am perplexed by what I'm seeing with Quark 9. The computers that I'm looking at have some private copies of some Helvetica fonts. A bunch of these fonts are also contained within /System/Library/Fonts/Helvetica.dfont, so FontBook complains about the duplicates. I'd like to ditch the files in ~/Library/Fonts in favor of the System versions, and every program except Quark 9 is happy with that.

It's the /System/Library/Fonts location. If I copy the Helvetica.dfont file into /Library/Fonts, then FontBook freaks out about all the duplicates, but Quark sees the fonts and offers them all up on the fonts menu.

Am I missing something? Is there some trick/preference/setting to get Quark to see the /System/Library/Fonts fonts? Some reason that it shouldn't?