This part is really key in the AVI Limitations for H.264 content, unless you want to encode without B-Frames, but then.. why?
Quote:
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AVI was not intended to contain video using any compression technique that requires access to future video frame data beyond the current frame (B-frame).
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The consequence of that is that AVI does not like frames to be in a different order then the display order, but for bi-directional prediction (B-Frames), this is required. So if you try to do that with AVI, it screws up your timestamps.