So what's in your site-init file?
Do M-x locate-library <RET> site-start <RET>
Library is file /etc/emacs/site-start.el
to find the file and take a look at it. You can send it to me and I'll
take a look, but if you feel like honing your skills, you can try your
hand at it. The basic idea is bisection: after copying the file to a
safe place, you take half the file, throw it away and see if the problem
persists. If it does you cut the remaining part again in half;
otherwise, you try the othe half.
Of course, you have to be careful about the cutting: don't cut in the
middle of the function e.g. And "half" is just a manner of speaking. If
you can throw large chunks of the file away and still get the problem,
then whatever remains is the culprit. Even if you don't understand why
something is broken, then you have made the life of whoever follows up
on it much simpler.
In your case, you probably want to check any changes to load-path.