Hello davidbraigh,
Thank you for your post and please excuse for the delayed answer.
Could you please specify what "Start X", "Start Y", "Width", "Height" of window settings have you chosen before the recording?
Have you uploaded your record using HyperCam or directly from the Youtube web-site?
It will be great if you could send us your record, which was not uploaded properly to Youtube. Could you please upload it e.g. to dropbox.com and send us the link?
Thank you in advance.