Hi mikek,
I just realised that having increased the z-index of the floating header, the flex menu then fell behind the header (floated). I added the following code (I've included your code) to the custom.css file which has solved the problem. Just thought I'd post this incase anyone else has the same issue.
#s5_header_outer.s5_floating_header {
z-index:10000000000;
}
#subMenusContainer{
z-index:10000000001;
}