Are you using the default skin or the 4:3?
When activated, both the GPS screen and video screens display in the wrong place. They are correct size, but located in the upper left corner of the screen. If you enter full screen, then return to normal mode, they are then in the correct position.
Also the GPS window (iGuidance for me) displays the menu bar ("file" "edit" "view") in both windowed and full screen mode. I don't know if this is a new or old problem.
I'm having the problem as well. I'm using iGuidance v3.0
When I use the eye to go fullscreen, and then go back to viewing Freeway, iGuidance is positioned perfectly. I don't mind having the toolbar there, so that's not really an issue. Although, Freeway will not position the iGuidance correctly when first ran.