The filters didn't work, they actually caused the same problem, only twice as bad.

I'm about out of ideas. I tried different versions of VDub, I tried different Mpeg encoders, I tried different codec settings. I belive the problem is in Vdub, because when I deinterlace in VDub, the flickering is gone. Of course, so is half my resolution.

I just tried resizing in After Effects, the same problem, thought to a lesser degree, probably because I didn't sharpen. I don't understand this at all! I will try different encoders again, but I had tried Adobe Media Encoder with a vdub file, and it still showed the problem the same as Hcenc. I am extremely confused. I'm too tired to continue tonight, but I'll post a video file tomorrow showing the problem.