It is very prominent with Nautilus and I haven't noticed this problem in
other programs (GTK and other).

That said,  the touchscreen in 12.04 is in general less reliable than in the 
previous version of Ubuntu. Symptoms are:
- it stops working in unity-3d after a couple of clicks (Bug #949791)
- unity-panel-service crashes sometimes when indicators are clicked with 
touchscreen 
- click helpers in onboard are not working when used with touchscreen
- right click emulation with mousetweaks is not working with touchscreen

No idea whether these problems are in any way related.

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https://bugs.launchpad.net/bugs/1002788

Title:
  Using the touchscreen breaks normal device left clicking

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