Multiple USB - JTAG devices, how to specify target over Xilinx XMD?
I know this is a bit old, but the solution was so frustratingly simple that I had to post it...

As you may have seen, you can specify the port to connect to using 

... -cable port &lt;port number&gt; ...


However, it seems that XMD will try to auto-connect and select the last connected JTAG device, which defeats the purpose of specifying the port.

The solution is to specify the cable type before the port number. For example:

... -cable type xilinx_platformusb port USB21 ...


You can try this out by using the xrjtagchain command and ensure that it connects to the proper port each time.