The part that is broken is the software in Kickstart 3.1 that opens a graphics library. If you do that and then "hit the hardware" with a POKE, DOKE or maybe LOKE, hopefully the screen data your game produces is interpreted right and you are sorted.
The part that sounds broken is Amos. It sounds like it's either doing something wrong when opening the screen or making assumptions about the copper list or memory layout.
The source code was released at one point, so it should be quite easy to work out what the problem is and fix it.