Did you try specifying where exactly you installed libmcrypt, e.g. --with-mcrypt=/usr ?
I believe you can find where mcrypt is on your system by typing locate mcrypt but don't quote me on that - I'm not knowledgeable with the Unix OS's anymore. 🙁
Likewise, you can try removing libmcrypt and then doing:
rm -rf /usr/bin/libmcrypt-config /usr/lib/libmcrypt* /usr/include/mcrypt.h
cd /usr/local/src
(substituting in correct paths as necessary) to ensure that it's completely gone before you re-install it and try to re-compile.