For clarity I think the issue is this:
Exported HTML5 or Node-Webkit projects reduce the scale of animated sprites by 50%
However as I said, I did fix it. I believe I solved my issue by doing one of the following things:
I say that because those are the only things I changed before re-exporting and that seemed to solve it.
I'm at work now, but I'll try to recreate the bug in a simple .capx later.