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Unfortunately, converting videos to MKV is not an option anymore. The game has been built with AVI videos, so changing the extension means importing the videos again in each scene. There are too many of them so we have to continue with AVI.
However, I think the encoding is not the problem. In Catyph, I have AVI videos in Xvid too, and everything works well. There is a video between each scene, and the game doesn't crash. So the AVI/Xvid videos are possible and I think it's an issue to be found in ASA only.