Bug reported at https://bugs.launchpad.net/ubuntu/+source/wacom-tools/+bug/295292
I verified it on my tablet Fujitsu T2020 with ubuntu 9.04beta installed.
COoLoSER contributed a script which saves and restores the calibration before suspend/hibernate and after resuming the system to fix the bug.
Hope this to be incorporated into the wacom-tools package and the source distribution.
PS: this script should be installed in /etc/pm/sleep.d to work.
A script to save and restore the calibration
Linuxwacom has moved from Sourceforge to Github. If this is still an issue please reopen this request there.