Would you be able to send us your InDesign file or a sample file that recreates the issue and your html5_output folder for us to troubleshoot? You can submit them here:
I don't know that I've seen that behavior where an animated gif is partially loaded and replays from the beginning. I'd be happy to take a look if you'd like to send us your files:
First, I'd make sure that you're using the most recent version of in5:
Using an image sequence sounds like a good idea too.
If it's a looping animated gif, then you could try recreating it as a non-looping animated GIF. There is code that you can add to make a non-looping animated GIF replay when you return to its page if that's preferred: