I figured helping with such little info would be difficult, so I made
a test. In the test, I made a video from a sequence of jpgs I
generated using transcode (and a couple other programs - but
transcode did the main bit). It uses square pixels, but I still see
the same behavior - first play runs through fine, loops are wrong.
Reloading the page is hit or miss - sometimes the first play works,
sometimes it goes straight to stretch mode.
here's the test:
You can download the video and see a source frame on that page.