Inserting an animated GIF plays fine in HTML5 but in flash versions the gif flickers.

We are publishing for HTML5 with a SWF fallback. We have been making animated GIFs pretty routinely and most work fine but several flicker when viewed as non-HTML5. Anyone have any workarounds? Really frustrated here. We've tried to output the GIFs in a ton of different configs, looing, non looping, dithered, non-dithered, different color depths, different frame rates, EVERYTHING. It's very frustrating.