Christian,
Sorry, I was confused. Some folks reported issues between USB3.0 and XDS200 emulators, not XDS100.
I see the TUSB8040 is a USB3.0 hub and unfortunately I don't have one here to test it myself.
Regarding the serial numbers, I assume you are appropriately setting up the target configuration file (.ccxml) to properly discern between the two, is that so? If so, can you try to manually launch the debugger and connect to each XDS100 so you can get a more precise assessment about where in the connect/load/debug the error is occurring?
Hope this helps,
Rafael