I see a few dodgy things going on here, none of which directly address your problem, but which MIGHT remedy it:
1) Do you REALLY want to render out at 640x360? As it's set, that's what you're going to get.
2) DO NOT USE THE AE RENDER QUEUE to make H.264! AE really stinks at it. In fact, I don't know how you even got AE to do it. Are you actually using Adobe Media Encoder? I'd render out something in a high quality codec like QT's in PNG, Photo JPEG, Animation or ProRes 422 codecs. Then let Adobe Media Encoder do the transcode to H.264.
3) There is absolutely NO reason why you should be getting multiple files. I assume you mean they're segmented -- :00:00 - :24:29, :25:00 - :58:29, :59:00 - 1:14:17, etc. If that's the case, that's just bizarre and you'll have to give us PRECISE information about your system -- OS version number & AE version number right down to the very last decimal, any third-party cards, amount of RAM, and storage for beginners. If, however, you mean you're getting multiple files of the same thing, it sounds like you are indeed somehow using Adobe Media Encoder, and you have it set up to make all those different files.
KGAN (CBS) & KFXA (Fox) Cedar Rapids, IA