When you install OS 3.9 do you apply all the Boing Ball patches and the post patches as well? Are you installing Cybergaphx 4 with latest patch as well/
What video card do you have? Does is support native Amiga mode promotion and are you using the correct output port?
Make sure you are selecting a video mode that the monitor card support.
Is this in your A4000T?
-Nyle