I have a system that utilizes both gpus and fpgas and I want to run one cgminer instance for gpus and another for fpgas. Starting in 2.11.0 with the new usb subsystem, I am unable to start an instance of cgminer for just the gpus. Whenever I try to start the instance for gpus only, cgminer displays "MTX: BitForce USB failed to get cgminer-usb..." and exits. Is there any way to disable the usb detection like how "-S noauto" used to work?
--hotplug 0
tried that and still had the same problem
Yep at the moment all BFL/MMQ devices are detected immediately.
--hotplug 0 will only stop it finding new devices when you plug them in.
I've decided on how to handle this already but not implemented it yet.
I'll move it further up the todo list

In the mean time, if you start the cgminer that uses the FPGAs first (with -G), then start the GPU cgminer 2nd with
--hotplug 0 then the GPU miner won't pick them up at startup or later via hotplug.