We have exactly tha same issue. We have an ASUS P8B WS motherboard with USB 2.0 and USB 3.0 controllers.
With ESXi 5.0, the USB 3.0 appeared as an unknown device but I could still attach it to virtual machines. since ESXi 5.1, the USB 2.0 does not even get detected. The USB 3.0 shows with its proper name, but after rebooting the box to apply the new settings, it shows as a non-passthough device. Even with the latest patch.
Attached USB devices have never appeared as passthrough devices, I could never select them.