So you have the same problem with Fvwm? How do you define your fonts? Gnome related stuff shouldn’t affect Fvwm in any way, even though it might affect programs running on Fvwm (like as you said gkrellm).
I had the same problem with the font in fvwm and I got it working properly!
gnome-settings-daemon affects the fonts display when you specify them as follows:
Font “Shadow=1 1 SE:xft:Comic Sans MS:size=12”
then to get the fonts displayed correctly just replace “size” by “pixelsize” and you’re done!
for gkrellm that was a bit more tricky as you can’t use this option the workaround is to add "+ I piperead “sleep 1” "to the Initfunction between the command for gnome-settings-daemon and the one for gkrellm!
In fact gnome-settings-daemon overrides your dpi settings when you use it. The correct settings can be found in /var/log/XFree86 (at least for me). Then the trick is to use gnome-font-manager in which you can give your dpi settings (it uses a to big value by default for me).
That is pretty good info too…but I found an other answer in the Gentoo forums post and it is great because you don’t have to change any of the main system files. However it is good to know that if you want to, you have to you can just change the startx script.
By the way, since I use Qingy to log in, I by pass the startx script so It doesn’t get read anyway. I will have to talk to him about that.