http://bugs.winehq.org/show_bug.cgi?id=14282
--- Comment #28 from evanh evanh@clear.net.nz 2010-01-28 18:51:41 --- I was just trying out various display modes to see if I could reproduce it and noticed that after a windowed in forced desktop then changing to windowed only I got a mismatch between the pointer position and where I was clicking. Subsequently fixed by selecting the one and only window size in Eve's selector. Maybe this is related or maybe it's a separate bug. Dunno.
Other than that, I got no visual offset in windowed mode.
Could this be a Gnome issue maybe?