a question about the pkg_add and "make install clean"

[well sun]

       I had install the freebsd5.3 with custom setup and only install
   the source code and base, not install xorg and perl. Then I use cvsup
   to upgrade stable source code and current ports. After doing these, I
   want to install the kde3 and gnome2. But I found when I use the
   pkg_add command, freebsd will go to the directory under "5.3-release",
   it is older than the installation using "make install clean" command.
   For example, when I use pkg_add xorg, it will install 6.7 version.
   When I use "make install clean", it will install 6.8.2 version. How
   can I make them to install same versions?  Another question is, when I
   install the xorg-clients, it give me a error message that "libc.so.6"
   not found, and many reference to *GL.so not found, how can I fix it? I
   had get the latest X11R7-src{1,2,3}.tar.bz2.
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References

   1. http://g.msn.com/8HMBENUS/2734??PS=47575