I presume you used custombuild to install apache and php? If so, due to the fact that you compiled php from source, you need to rebuild it after adding --with-xmlrpc to the list of configuration arguments.
This is the place to add it;
/usr/local/directadmin/custombuild/configure/ap2/configure.php5
After that run ./build php inside the custombuild DIR.
Hope this works for you.
cd /usr/local/directadmin/custombuild
mkdir -p custom/ap2
cp -fp configure/ap2/configure.php5 custom/ap2/configure.php5
#add your --with-module line to the end of the custom/ap2/configure.php5 file,
# and make sure the \ character exists at the end of all lines except the last one.
./build php n