Which (and how many) FPGA devices and what sort of computer CPU (netbook, low power, ?) do you have?
I suspect with ASIC that will get worse - i.e. whatever problem your computer has with the small amount of USB accesses at the moment, will only get worse as that increases with ASIC devices.
With ASIC, cgminer will be hitting the USB port a lot harder.
USB shouldn't have this problem with the low amount of USB access occurring at the moment.
Is it every 5 seconds? Is it every key? Or is it once in a blue moon?
Edit: also what is your USB layout - hubs, multiple motherboard ports, etc.