If you compile Qt Creator against the current 4.8 branch you will recognize that on Ubuntu 11.10 all mouse input is forwarded to the application ~30 pixels above. That makes usage of the whole application (specifically menubars) impossible. If you compile it against the current 4.7 everything works fine. Hence this is a 4.8.0 regression.
Jason also mentioned that he can reproduce it on his Ubuntu 11.04, hence this is not related to the latest release.
To get rid of this misbehavior, unmaximize the window and maximize it again. Then mouse input works as expected. So this is probably relate to the Unity menubar.