This time rather than upscaling the video, I recorded everything full dimensions and whittled it down to size. This may or may not lead to better quality, I can't decide and really the other one looked pretty good as it was so I'll probably stick with that.
Also: never try to play Stalker, record Stalker, leave TF2 running in the background, host a Skype call, and be encoding videos at the same time. It doesn't lend itself to good framerates.