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When Ubuntu 12.04 starts on my X201T the touchscreen works fine, I can touch anywhere and the mouse will appear there. However once I log in to the desktop the touchscreen starts acting like a touchpad. if I touch the screen it acts like a permanent left click, and if I move my finger on the left side of the screen with the mouse on the right, it will follow my motions with a slightly larger motion, much like a touchpad on high sensitivity. Touching in random locations does not make the mouse appear (or jump to a new location like a miscalibrated screen).

Any ideas?

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It seems that your touch device works in relative mode. You need to switch it to the to absolute mode -- the same as your stylus. To do this try:

xsetwacom set "Wacom Serial Penabled 2FG Touchscreen touch" mode absolute

Note that your name of the device might be slightly different (this is from X200T). To list your devices run:

xsetwacom list
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