Hi Kokoszka, Are you filming this with a DSLR? If so you probably need to use photo-jpg codec. This is for the progressive format. You will find that this may cause banding or your video may play back choppy. If it plays back choppy it's not the end of the world. It means your computer can't quite handle the large video at 1080p. Open it in a video player and skip through each frame. If there all there then no problem and start uploading
Remember don't do %100 quality as this will make the video stupidly massive. Go to %95-%98
If your video is looking squashed make sure you have sqare pixals whilst rendering your video. You may have HDV setting which is rectangular pixels and so your footage will look squashed!
Hope this helps! Once you've figured it out once (may take some time) you'll be up and away!