Problems with aspect ratios

[Ibsen]

If I make a DVD of an .avi file that's originally neither 4:3 nor 16:9, there are black "boxes" in large white areas, especially in fast-paced action scenes. They vanish after a couple of frames, but are really annoying. I suspect that the problem is somehow related to transparent colors and black bars in the final movie.

Has anyone else had similar difficulties? Any ideas how to fix that problem? I've used QuEnc 2-pass encoding. I think I will try a different encoder, maybe it could solve the problem.

Edit: I'm using beta 0.4.1, my OS is XP professional.