Right - if you export as a video (into .mp4, youtube 720 format) in videopad and then upload that video file directly in youtube then uploads in 2D correctly. The video file created by Videopad is 2D as well.
So that works as a work around - it looks like the problem is within the inbuilt youtube uploader in videopad.
Youtube used to have a checkbox that you will check if the video you were uploading is in 3D. It now doesn't have that and relies on the metadata within the videofile to identify if is in 3D format. Perhaps the videopad youtube exporter/uploader is encoding the video with that metadata in, which is why youtube recognises it as a 3D video?
What's strange is that whatever encoder videopad uses to export as an .mp4 in "youtube 720" format (which I think is the same as the inbuilt youtube exporter/uploader uses) must not include that data. Maybe it's the uploader part of videopad that does?