Similar problem here, I was not able to use touchpad-/mouseclicks e.g. in "Save 
as"- and "Scale layer"-windows.
The solution for me was to set the mode of all devices to "disabled" in the 
extended input devices options, only device working in "window"-mode is the 
Wacom Graphire4 stylus. Now everything seems to work fine here.

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Can't click on UI elements in gimp (intermittent)
https://bugs.launchpad.net/bugs/556670
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