If the binary contents of archive you're uploading changes substantially between uploads then the patching tool may not be able to find any reusable blocks to use. This could just behow Unity is generating HTML5 builds, and there's not much we can do about that. Maybe there are options with the build tool to make it have a more consistent output?
Thx for replying. Yes I figured it might just be endemic to Unity and yes I'll look into whether there are options. I was also curious whether it was a known situation. I can't guess how many Unity builds your wonderful platform receives every day but figured if this was a consistent pattern, someone might have special-cased it!