When I look at the schematic of the BlackIce-II, I see that there is a single VBUS signal that goes to the USB Serial Monitor connector and the USB connector that's located in the "USB & Power Supplies" section of the schematic.
The Getting Started Guide on github, has the following sentence: "If you are also using the second USB connector for debugging with the FPGA..."
This implies that it's ok to connect both USB ports at the same time.
But VBUS is a required feature per USB spec: it always needs to be there. And there are no guarantees that the VBUS voltages on USB 1 and USB 2 will be identical. They could be connected to different PCs.
Since VBUS is driven by a low impedance source, doesn't this essentially result in a short circuit condition?