The Display Size setting in the /etc/X11/XF86Config-4 config files is very complicated. Suffice to say that the 'rules' state that all themes should run as 100dpi.
Add this line -
Display Size 204 153 # 100 DPI @ 800x600
under the "Section Monitor" of your /etc/X11/XF86Config-4 file and all should be well.
However, this made all the big fonts HUGE, so I used -
Display Size 271 204 # 75 DPI @ 800x600