It's a monitor DPI thing. I had the same problem when I switched from driver build 769 to whichever build was after that one. With 769 and earlier, the nVidia X driver didn't report the DPI properly (and I thought it was just fine the way it was... whatever), so KDE 2 thought it was 75DPI. So its 14-point font was just about the right size for a window title.
When I went from 769 to whatever the next release was, the X driver did start reporting the DPI properly (it was closer to 100DPI than 75), so all of a sudden the KDE 2 14-point font got gigantic. So I made KDE use its 8-point font instead, which ended up being just about the right size.
Of course, I've since stopped using KDE, but DPI was my problem. Maybe it's something similar there? Can you make your desktop environment (or window manager, whichever one you run) use a smaller font for decorations?
You might also try looking at your font path (xset q | grep X11R6 should tell you the current font path), and seeing whether the 75DPI font directory is in front of or behind the 100DPI font directory. Moving it behind the 100DPI directory (which is accomplished by removing it and then adding it at the end of the path) should help:
xset fp- /usr/X11R6/lib/fonts/75dpi/
xset fp+ /usr/X11R6/lib/fonts/75dpi/
If the xset q command doesn't print anything, then you're probably using xfs, the X font server. There's probably documentation somewhere on how to change which directories xfs looks for fonts in, and in which order, but I don't know where it would be, or how to do it. I don't use xfs...