Hi Rafael,
I have simplified my setup and removed the TUSB8040. Instead of using a kit with two XDS100v2 on-board, I'm now using two independent kits (TMDSRM48USB and TMDX570LS31USB) connected to the same USB Root Hub at my PC.
I have a program in these kits which flashes some LED's, so I can see to which kit I'm connected by simply Suspending the MCU.
When I connect these two kits to a on-board USB 2.0 controller I can connect to the two kits independently, when I connect them to the PCIe USB 3.0 controller I'm only able to connect to one of the kits.
So I assume my configuration is correct, as it works with USB 2.0 but not with USB 3.0.
One additional point, as I'm not using a CCS project for these tests, but pure CCXML files, I'm always connecting manually to the targets.
This should now be a setup which you can easily build up on your side. But please be aware, there are some Intel XHCI (USB 3.0) Controllers which have an additional EHCI (USB 2.0) Controller for the same physical USB plug at your PCI and these seem to switch to EHCI mode in case a USB 2.0 device is connected instead using the XHCI controller as my Renesas and newer Intel controller do. In the case these have switched to EHCI everything just works fine.
Thanks,
Christian