I have the same problem in ST2 and the latest ST3. Windows 7 x64. Restarting has no effect. Disabling all but the main mouse device has no effect.
Clicks on the menus, folders, scroll bar, thumbnail scroll bar, and expand/collapse icons works like normal. Left/right clicks and scroll wheel in the text editor and line numbers are ignored. Artificial clicks from Windows accessibility tools and Autohotkey are also ignored.
ST2 has worked fine for years on this system until recently. How much additional money do I need to pay to prioritize a fix for this issue?