I'd wait and see if you get an official response, but what works for me when I have a
very specific clip from a very specific device, that causes incompatabilities, I go and find ffmpeg on my hard drive. I mostly use a video editor myself, if you do I would try re-encode the clip, and open the new file in hyperlapse pro. Hyperlapse
works fine with my Sony, but my video editor hates me if I set it to record in 25fps. But ffmpeg will let you re-encode without converting to a different size or framerate (convert just changes the package/container, don't try convert to mov or wmv,
that won't really help).
ffmpeg is a trial and error thing, so I've not got a recipe.
automation of testing the stuff dude