I've noticed that prepare-kernel-sources script contains a malformed 'cp' command in the second half of the script.

VER=`uname -r`
echo "[*] apt-getting linux-source..."
apt-get install linux-source
cd /usr/src/
echo "[*] extracting sources, please wait"
tar jxpf linux-source-$VER.tar.bz2
echo "[*] doing stuff..."
rm -rf linux
ln -s linux-source-$VER linux
cd linux
zcat /proc/config.gz > .config
cp /boot/
make scripts
make prepare
ln -s /usr/src/linux /lib/modules/$VER/build
echo "[*] tada!"

I wonder if that 'cp' command was supposed to copy kernel config from /boot. The script appears to unpack the kernel sources nevertheless.