To start, I have recently built the new computer which I am now using. It is running:
AMD Athlon 64 X2 Dual Core 6000+ Processor
Nvidia GeForce 8800 GT
Windows Vista Ultimate x64
(The rest of the hardware is more than likely irrelevant.)
The process:
I use DVD Decrypter (Probably not the latest version, but I don't think this is the culprit.) to rip a DVD.
I use DGIndex to create a D2V project.
In AVISynth, the AVS file has a single line: mpeg2source("C:\DVD\FILE.d2v")
I open it in VirtualDubMod, and here's the results...
The Results:
I first notice the problem with Higurashi no Naku Koro Ni

Haruhi (Ripped on my previous computer, but never had this issue on that one.)
DVD Resolution

16:9

So, resizing won't help.
I ripped Dragon Half the same night I ripped Higurashi, and I got:
DVD Resolution

4:3

Dragon Half is completely free of the problem. Could it only be 16:9 footage that is effected?
Next, I ripped Nuku Nuku, which is also 4:3
DVD Resolution

4:3

Well, apparently not.
Why would Dragon Half be immune to this problem? Is Nuku Nuku really 4:3? (I could swear it is, I am gonna check. It's not printed on the disc or case, which is annoying. I remember it being 4:3, anyway.)
Anyone have any ideas as to why this is happening? My searches on the internet have only turned up people having trouble playing back videos using XviD, which is apparently solved by turning on some kind of "compatibility mode" - And I can't do that with this, because I am using avisynth, mpeg2source... I have some other things to try, but I am just about at my wits' end.