First off, I'm using the most recent version of VBA-M for Windows, that being the one at this link.
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Okay, here's my problem. I've been making videos of a playthrough of Pokemon Emerald for a Let's Play! sort of thing. Initially I played on the original VBA emulator and recorded AVI files directly using the emulator, and things worked out fine. I just had to compress the resulting file in another program and they'd be good to go.
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However, once I started using VBA-M (on the recommendation of the MOTHER3 Fan Translation, no less), I realized that recording AVIs turned out... weird. Namely, the result would look like this. And also this. I even made a video, if that would help at all.
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I can fix the problem manually using a program called Avidemux, which has a filter for this sort of thing. But it's a bit inconvenient to have to go out of my way to do that. So, um. If anyone has any idea what's going on and how I could fix this, that'd be awesome.