What USB Devices have you tried? It could be related to that. I know my Spider doesn't auto-mount the USB stick if it's already plugged in when I turn the Amiga on. But works if I unplug it and plug it back in. I haven't had it cause any lockups though. But then I also have a 4000.
My other guess would have been the power supply, but if you have an ATX one, that shouldn't be it. But then again, if you have a low wattage, or bad quality one, that could cause it to freeze, since any USB device is going to draw more power.
slaapliedje