That is certainly very unusual. The fact that it only happens in windowed mode does seem to point to some display setting, or a driver. Still may be worth checking graphics & display drivers.
It might help to set windowed mode & resolution via command line, just in case the resolution is the culprit. To do this:
Launch in windowed mode and force a lower resolution via command line: In Origin, right-click the SimCity icon and choose "Game Properties" > click the "Advanced Launch Options" tab > type "-w -r:1600x900" (without the quotation marks) in the "Command Line Arguments" box. Note: Use a resolution that your display supports. You can test which resolutions work best for you. Some examples: -r:1600x900 -r:1024x768 -r:1920x1080