I used to play Anno 1404 in P5 and that worked fine. I've upgraded to P6 and now I have screen flicker like other users have reported. But I also have weird looking graphics. I have posted a problem report (#6689449) to illustrate the problem.
Kees, Thanks for reporting this. The problem is that Snow Leopard Graphics update subtly broke Z-buffer for ATI/AMD graphics chips. This will take some time to resolve, sorry.