Decoded .avi's jittery at certain points

[eisnerguy1]

So, there's a point in converted avi files where it gets all jittery. From what I can tell, it's the same spot where the 3D effect kicks in during the original .moflex. Is there any way to avoid this? Love this tool by the way :D

[Gericom]

Might be possible if the format changes within a stream. I didn't know that was even possible

[eisnerguy1]

If it helps at all, I'm trying to convert the videos from the Pikmin Shorts. There are a few videos that are exclusive to the 3D version and not included with the HD version.