Hello,
I'm working in Pd extended using the planetccrma package, on Fedora 12, comparing behavior on two systems.
I found on one system all the iemgui fonts appeared correct, but the normal object fonts appeared too small (which is the opposite of usual; normally the object fonts are correct and the iemgui fonts are too large), but only when logged in using GNOME -- fluxbox made things bad again.
Also on a machine with the identical setup but a different monitor, even in gnome the iemguis appeared too large again. The only two differences between my machines were the X11 DPI setting (xdpyinfo | grep resolution gave me 75 on one and 96 on the other) and the gnome DPI settings under System->Preferences->Appearance->Fonts->Details->Resolution . As it turns out, if the gnome one is set to 72, the patches look the same as on other operating systems, except the object fonts are too small (I could fix this by editing the sizelist hack in pd.tk back to "normal"). Also, in fluxbox, the only way to get iemguis to look correct is if I run /usr/libexec/gnome-settings-daemon. I don't know tcl/tk well enough to know what all this means, but it seems the X11 DPI is meaningless to Pd, at least on my systems; I can make patches look normal (but fonts in other applications way too small) by setting the gnome DPI to 72, and resetting the sizelist hack.
I hope this is a little useful.
Matt