I noticed an interesting case when running Windows 7 with KVM and passing through one of my USB-3 controllers. The controller has a single port and a 3.0 hub connects to it. When I connect a USB-2 hub to the 3.0 hub, DPC latency spikes through the roof because of the interrupts. Even if there is nothing plugged into the second hub.

I wasn't sure if this was an issue with KVM, USB-3 or just a general issue with nesting hubs (even though I'm running low speed/power devices and a 3.1 port should be able to handle it) but you make it sound like it might indeed be an issue with USB-3