Weeelllll, here is the update:
I downloaded the HuffYUV codec, and whenever I converted a video with it, the computer would lock up upon seeing the dand ICON for the video. I have no clue if I did something wrong or what, but I've stopped usin that codec.
Somebody suggested Lagarith, and that has been working so far. I haen't tired it with all of my footage yet, but it works with what little I have tried.
....Maybe this should be stickied or something so Scintilla does not have to post that banner everywhere; I see i'm not the only one who has had this problem ^^;