I observed that XFree86-4.0.3-3 (and -1) produce larger fonts in netscape
buttons, netscape menu-bar, and every other Xlib only application. Gnome
applications are not affected (i.e. gnome-terminal menu bar kept the same
font). Stock wolverine XFree86 does not exhibit this behavior.
Most likely, your configuration somehow changed from using 100dpi fonts
to 75dpi dfonts or to some other font type. Check your font configuration
both in Netscape, and in xfs as well. Make sure xfs is running.
Did you find any problems with your config?
That was it. Somehow a line of /usr/X11R6/lib/X11/fonts/100dpi:unscaled had
crept in. After removing it, all seems back to normal.