When installing XFree86-ISO8859-9-2.1.2-13 a file /usr/share/fonts/ISO8859-1/misc/fonts.alias will be created. In this file there are entries like | fixed -misc-fixed-medium-r-semicondensed--13-120-75-75-c-60-iso8859-9 conflicting with the original XFree86 fonts (in /usr/X11R6/lib/X11/fonts/misc). So you will get multiple entries for font `fixed'. When using `xterm' this identifier will be used to determine various fonts and you will get probably the wrong one (I have seen it at umlauts). I suggest to remove such duplicate aliases or to comment them out in the *ISO* packages. ISO8859-2 and ISO8859-7 seems to be ok; but KOI8-R has the problem too.