Something about how the web build compiles everything vs a normal executable in windows caused the game to behave differently in our submission. If we submitted a download instead the game physics would work closer to how we expected them to.
Ah man that's a shame, hate to see it happen. I had something similar happen with my game, an add-on I was using didn't have web support at all so I had to take it out and patch a bunch of problems just before submitting.
Lesson learned, submit early and test often. Hope your next one goes better!