This might be a bug, or more likely a lack of understanding on my part but I
try to set up mcrypt with
./configure --with-libmcrypt-prefix=/home/qsys/libmcrypt-2.5.8/lib
it looks for
/home/qsys/libmcrypt-2.5.8/lib/bin/libmcrypt-config when the file is
/home/qsys/libmcrypt-2.5.8/lib/libmcrypt-config
i.e., it appends /bin to the path.