When operating on a Flash device in BPI mode, some of the options will still function on the FPGA. The "Get Device ID" and "Get Device Signature / Usercode" will apply to the FPGA, not the Flash. This occurs whether or not the Flash is selected.
This problem has been fixed in the latest 9.1i Service Pack available at:
The first service pack containing the fix is 9.1i Service Pack 2.