You've probably fixed it by now, but thought I'd post a suggestion anyway.
It might be due to the fact you have 2 versions of apxs on your system and it's finding the wrong one. This is usually when you have had a pre-installed version of Apache which may have put apxs in /usr/sbin/apxs.
When you install another, from source site for example, this may default to a different directory, and put apxs on as /usr/local/apache/bin/apxs
If this is the case, your configure command should look something like this:
./configure --with-apxs/usr/local/apache/bin/apxs --with-mysql --with-xml
HTH
