hmmm redownloaded both from kolivas and yours.

wget http://ck.kolivas.org/apps/cgminer/3.1/cgminer-3.1.1.tar.bz2
tar -jxvf cgminer-3.1.1.tar.bz2

pi@raspberrypi ~ $ cd cgminer-3.1.1/
pi@raspberrypi ~/cgminer-3.1.1 $ CFLAGS="-O2 -Wall" ./configure --disable-opencl --disable-adl --enable-bflsc --enable-bitforce --enable-icarus --enable-avalon

make

still says 3.2.1


then
wget https://github.com/kanoi/cgminer-binaries/blob/master/RPi_32/cgminer-3.1.1a
mv cgminer cgminer.old
mv cgminer-3.1.1a cgminer
chmod +x cgminer

still says 3.2.1