mac or pc?
...it is most likely suitcase to be the problem, you use fusion?
...many mac users report problems (like me, especially on intel) with quark and suitcase fusion, some go as far as ditching suitcase all together and using linotype fontexplorer instead (like me)...
...if suitcase has font activated and quark won't see it, you usually have to quit and restart quark once, twice if not three times...
...best you can do is keep suitcase up to date and quark as well see if that helps if not already...
...keep your font cache files clean on a regular basis and also limit the amount of fonts in your system folder to only the basic ones your system came with...
...the other option is to do what i did if on mac and switch to fontexplorer pro as it is much better...
andrew