Ok, so I finally solved it. I had to have the package libusb-dev installed.
This is what I did:
1) I downloaded the source and the new device file from Archlinux, unzipped it, and compiled it.
2) Copied the executable and the device file to another folder (according to the readme-file).
sudo cp pk2cmd /usr/local/bin/
sudo cp PK2DeviceFile.dat /usr/share/pk2
3) Changed user privileges to the binary (before doing this I had to run pk2cmd as root).
sudo chmod u+s /usr/local/bin/pk2cmd
4) Updated .bashrc with the line.
And now it works :)
mikael@computer:~$ pk2cmd -?v
Executable Version: 1.21.00
Device File Version: 1.63.148
OS Firmware Version: 2.32.00