Description of problem: The _AC_PATH_X_DIRECT macro looks for X11/Intrinsic.h, which no longer appears to be shipped by xorg-x11-proto-devel and thus not a good choice for finding the X11 headers. Perhaps X11/Xlib.h? Version-Release number of selected component (if applicable): autoconf-2.59-5.1
This was pointed out in the Debian Bug Tracking System: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=327655 and a patch was applied upstream: http://lists.gnu.org/archive/html/bug-autoconf/2005-09/msg00024.html
fixed in autoconf-2.59-6
pkgconfig should be used to detect the presence of all of the X libraries, SDK, font-utils directories, and various other things. When in doubt, assume there's a pkgconfig file or variable that does the job. ;o)