I have two ubuntu installations side by side on a sony VPCJ128FG on the same HDD, namely Ubuntu 11.10 and Ubuntu 12.10.
This problem is specific only to Ubuntu 12.10, (I'm writing using 12.10, No problems with the 11.10 version).
Everything works just fine after login into my user account in Ubuntu 12.10 if I do not use the touchscreen of this desktop. Mouse single and double clicks are okay and work as expected. The problem starts only after my touchscreen is invoked by a finger touch or even a fly touches my touchscreen . After that the mouse double click stops working. Nothing happens when I double click on folder icons in nautilus. Even right click on folders in nautilus with mouse is also does nothing. But I can still drag select the folders with left mouse click, which is the only thing I can do in nautilus then. Menu can be clicked though as expected.
This problem existed on this machine in 12.04 also. So I did a fresh install of 12.10, and got the same disappointment again. What is wrong with the touch drivers I can't figure out myself. Searched through threads could not find any working solution.
This problem is persistent on Unity desktop, so I installed gnome shell but still persistent, installed then Cinnamon and still no help. So I believe that the problem is related to something else.
One more thing I noted that (after invoking touch screen) when I hover the mouse (without any click) in the bluetooth or network settings windows, the text automatically gets selected. And there is perfectly no such problems while using Firefox or Google Chrome browsers. I can use mouse within the browsers still perfectly.