It seems that for the device that I have (Bamboo small SE), the mode of the axis are reported always as being relative, even though the device is actually in absolute mode. Changing the mode of the device is not reflected in the axis modes.
Do you mean shows up as absolute in output of "xinput list 'touch_device'"? This is on xorg 1.9.3 (Fedora 14) and xf86-input-wacom-0.10.11.
It seems maybe an xorg bug. If you change a device from relative->absolute->relative then xinput starts showing right value. The behavior is always what ever xf86-input-wacom requests regardless of xinput display values.
I want to say I also saw same output from synaptic touchpad and xf86-input-synaptics as well... but don't quote me on that part.