I've not had good luck with onboard USB 3 controllers, even with the version of 5.1 that lets pass through work for one boot.  I tried it on an Intel DQ77KB motherboard and I couldn't get it to work right.  It seemed that even though there were two controllers on that motherboard and I only tried passing through one of them, all of the USB 3 ports became inaccessable to ESXi no matter which controller I tried (i.e. no keyboard and mouse), and also none of the ports ever became available to the VM.   I ended up buying a Startech mini pci express USB 3 add on card and that worked fine.

I haven't tried 5.5 yet, as I won't be back to where that computer is for several months, so I won't get to try it until near the end of the year.