I also have had quite some problems with linux and the FCD. It appears that is is related to bandwidth reservation of the USB bus. The FCD is a USB 1.1 device which is 12Mbit/s. As you are probably running it in a USB 2.0 port so there is a USB 2.0 to USB 1.1 arbitration unit in the USB interface chip.
The linux kernel has to allocate the bandwidth to each device USB 1.1 device on the USB 1.1 arbitration hardware and as the FCD runs at 96ksampes/second consumes a significant amount of USB 1.1 bandwidth. For memory linux requires a contiguous allocation of the USB 1.1 bandwidth for the USB device and if you a have keyboards and mice (which generally are usb 1.1) then this fragments the USB bandwidth allocation table.
If this is the case you can try two things:
1) remove everything else from the USB bus especially keyboards and mice.
2) switch to a USB 3.0 port which seems to be better specified but INTEL and the software to drive it is better/more-consistently written. It handles USB 1.1 arbitration better.
I opted for #2 and FCD seems to be working fine on linux for me.
Windows seems to do a better job of USB 1.1 arbitration/USB bandwidth allocation so yes my FCD worked in windows but not in linux.
I did look into the USB software on linux with a view to fixing it but ran away crying when faced with the complexity and the possibility that each USB chipset vendor can "do it differently" USB 2.0 is a box of hammers!!
I recall than is was also heavily dependent on the USB silicon vendor on our PC and which USB hubs/devices you have connected so what works for some, didn't for other etc etc.
It is a shame as I really like the FCD, but the fact that it is USB 1.1 is a real bummer for plugging and playing on linux.. I found.
As always your mileage may vary and with this particular problem you are almost guaranteed it will.
Here is a bug report for GQRX that details it, although the issue is not with gqrx but linux kernels treatment of USB devices.