i have issues with the window mode since Unity 4.0.1f2. When i build with the new version of unity i get an offset between mouse cursor and button highlight. also the window is not position correctly on maximize, see attached files.
I send a bug report too. So if someone hast the same problem or a solution for it, let me know. thx.
I have seen issues like this happen with buggy video drivers when running aero on windows 7. Might try updating your drivers and turning off Aero to see if that is it, and reporting that with your bug report.