I'd be checking how flat the big board fits over the glassed support area. You may need shims in a few places. (Little clay balls can be used by putting them in areas that appear low with a straightedge. Install the floor board then take it off and see how the balls differ.)
But even just inspecting the support
fiberglass with a longish straight edge can be a good diagnostic tool. One would think you wouldn't need those 'under boards' at all, but having them in there could solve the problem by reducing flex in areas that aren't sitting down on the glass....?
Bottom line: Usually creaking is a matter of movement, eliminate any flex or movement.