VNC Server uses VNC Mirror Driver by default to improve performance. VNC Mirror Driver does not support Aero effects. This is a known issue with all mirror drivers (as discussed in Microsoft forums).
When VNC Viewer connects to VNC Server, if VNC Mirror Driver is enabled and Aero themes are in use, the colour scheme is changed to the Windows Basic theme. This can have some unpredictable effects, as window borders are different in Aero and Basic. This causes windows to be slightly resized, which may cause their maximization to change. When connecting to a VNC Server computer with multiple monitors, the window may be moved from stretching across monitors to fill only one monitor.
Depending on the application running on the VNC Server computer, disabling VNC Mirror Driver can resolve this. Test with your application by changing your VNC Server > Options > Expert tab > UpdateMethod parameter to 0 (for VNC Server versions prior to 5.3.0) or CaptureMethod to 1 (for VNC Server versions 5.3+). Polling will be used, so this may have an impact on the performance of the VNC Server machine. Additionally, changing the desktop theme to Windows Basic will solve the issue for some applications.
Finally, for some applications, such as Windows Media Player or Microsoft PowerPoint slideshows, disabling connection notifications is required, otherwise fullscreen video mode will be exited when a VNC Viewer user connects. To disable connection notifications, open VNC Server > Options > Expert tab and change ConnNotifyTimeout to 0.