The files /usr/X11R6/lib/X11/fonts/100dpi/fonts.dir and /usr/X11R6/lib/X11/fonts/75dpi/fonts.dir both list fonts that aren't actually included in the XFree86-100dpi-fonts or XFree86-75dpi-fonts package. It could be argued that that's a bug, but the more significant bug is that the xfs startup script doesn't compensate for this problem by running mkfontdir before starting xfs. Logic has been added to the script to only run mkfontdir when it is "needed", but one case where it is "needed" is not detected in that logic -- when fonts are listed in fonts.dir which don't actually exist in the font directory. I will attach a patch that adds this logic to the script.
Created attachment 21246 [details] patch to /etc/rc.d/init.d/xfs to rebuild font dir if fonts are missing
The fact that xfs regenerates fonts.dir, fonts.scale on startup is already rather questionable. I believe extending this behavior would be a bad idea. (The current script has the slight problem that if you have a directory with mixed Type1 and TrueType fonts, your fonts.scale will be overwritten.) The problem is simply that an incorrect fonts.dir was packaged, and I believe this has been fixed now.
I am not sure exactly how I would like to see this handled, so I am defering it for the future. We'll come back to it some other time.