xfdesktop uses a symbol from libX11 without linking directly to it. 

/usr/bin/ld: ../common/.libs/libxfdesktop.a(libxfdesktop_la-xfdesktop-common.o): undefined reference to symbol 'XInternAtom'
/usr/bin/ld: note: 'XInternAtom' is defined in DSO /usr/lib64/libX11.so.6 so try adding it to the linker command line

It should link directly to libX11 there in case whatever depends on it now stops doing so. 
See: 

https://fedoraproject.org/wiki/Features/ChangeInImplicitDSOLinking
for more info. 

Here's a hacky patch to fix it, but you will want to add it more properly in the automake files. 

diff -Nur xfdesktop-4.6.1.orig/settings/Makefile.in xfdesktop-4.6.1/settings/Makefile.in
--- xfdesktop-4.6.1.orig/settings/Makefile.in	2009-04-14 15:54:05.000000000 -0600
+++ xfdesktop-4.6.1/settings/Makefile.in	2010-02-14 10:22:21.000000000 -0700
@@ -171,7 +171,7 @@
 INTLTOOL_XML_NOMERGE_RULE = @INTLTOOL_XML_NOMERGE_RULE@
 INTLTOOL_XML_RULE = @INTLTOOL_XML_RULE@
 LD = @LD@
-LDFLAGS = @LDFLAGS@
+LDFLAGS = @LDFLAGS@ -lX11
 LIBEXO_CFLAGS = @LIBEXO_CFLAGS@
 LIBEXO_LIBS = @LIBEXO_LIBS@
 LIBEXO_REQUIRED_VERSION = @LIBEXO_REQUIRED_VERSION@