FWIW, when I ran into this, the problem turned out to be a parent div with -webkit-transform: translate3d(0, 0, 0) in its CSS. Apparently, this is a known source of potential mayhem in child elements with position: fixed.
For what I was trying to do (turning fixed on and off as a way of sticking a key nav element to the top of the page as it scrolled by), the solution was to append it to the page body element when it was time to hold it in place and sticking it back in its wrapper div when it wasn’t. No idea if any of this would have helped the OP, but if you’re chasing this bug yourself, worth looking into.