What is the ToolType VooDooInit? I've never come across that one. No mention in the WHDload docs.
What is your video setup like?
How is Amiga Native gfx displayed?
Scandoubler + switcher?
Dual input Monitor?
Two monitors?
Composite to TV input?
LCDTV?
Is there no chance that you are just "looking at the wrong screen"?