I've been starting to get this NAK Timeout a lot recently, I never had this problem originally it's only since I changed from the Clockport version of RapidRoad to the non Clockport version in my A4000, it seems to be with certain USB devices though such as USB pens and not CF cards in my card reader. The Pens worked fine before though. A few powercycles in Poseidon seems to fix it but it's pretty annoying. I have WE040, RTG, etc in my A4000.
Strange because it used to work flawlessly, I'm suspecting a power issue maybe? Perhaps I have too much hardware for a standard A4k PSU? Yes my RR is connected to an XS-100 and it happens in ZII and ZIII mode.