Might be video hardware/driver issues. Try lowering hardware acceleration settings, like overlay.
Also, a smaller video is not like a smaller archive. It isn't "more compressed". A smaller video has a lower bitrate (less data = less visual detail/quality), and is generally easier to decode. Generally videos today are what I would refer to as "over-bitrated", as they like to really bloat things. I mean, 220-240MB for a 23 minute anime?? Even at full DVD resolution I can do way better. Of course I use Divx Pro at max, so its slow to encode (but not decode) and its high quality. Maybe they're just lazy and are upping the bitrate to compensate? "We've got to encode all 300 episodes tonight!"
Anyway, what I'm trying to get at is that you need to throw a 1000+ kbit video at it and see how it does. Try it with ffdshow if you haven't already, I'd be curious to know if there is a performance difference.