wacomcpl write the calibration into ~/.xinitrc but some popular desktop distributions such as ubuntu/gnome or something else never executes it on user's logging in. How about writing the calibration into /etc/xdg/autostart/wacom.desktop or so for the window manager to reset the calibration correctly?
Linuxwacom has moved from Sourceforge to Github. If this is still an issue please reopen this request there.