Try zeckensack's Glide wrapper, then detect the available cards in FS setup... see if you can do Glide and maybe that will fix it. What OS?
EDIT: In zeckensack's configurator (Start Menu, under Glide Wrapper), try doing "application-specific overrides" and setting it for Descent: FreeSpace.
EDIT2: To make FS Setup detect Glide in WinDOwS 7 (most likely Vista as well), you must needs to set its Compatibility Settings (right-click>Properties>Compatibility) to WinDOwS '98. Seeing as I have UAC disabled, you may need to set it to run as Administrator as well, but I can't tell.
EDIT3: This seems to get the game to work for me, and I can see all the fonts; however, I now have invisible ships. HOWEVER, I'm using the GOG.com version; this might work for your install / system configuration. Try and see.