Figured it out. Being new to compiling I just learned that the library I was creating was going into /usr/local/lib while the system was trying to use the older version installed with the distro in /usr/lib. After trying several methods of getting the correct libtorrent to be used, this command worked for me:
PKG_CONFIG_PATH="/usr/local/lib/pkgconfig" ./configure --with-xmlrpc-c
Don't know what it really does but as long as it worked.