Wacom drivers and screen output rotation should work in pair in both cases:
rotate screen output and digitizer input when user set screen rotation in 
screen resolution settings;
auto-rotate screen output and digitizer input when convertable laptop is 
converted into tablet mode.
This bug-report concerns the second case.
There's another bug-report, that concerns the first case: 
https://bugs.launchpad.net/ubuntu/+source/wacom-tools/+bug/288231

Here's link to a bug-report for IBM/Lenovo that contains auto-rotation
scripts with 3D accelerometer support:
https://bugs.launchpad.net/ubuntu/+source/acpi-support/+bug/159026

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Rotate Screen in TabletPC stylus and pointer mouse not coincidence
https://bugs.launchpad.net/bugs/217182
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