Does it appear at start-up or occasionally whilst the app is running?
This could be the Flash App and the Time App interfering with the Config App as they all query the USB device. Does it happen with just the Config App running?
Every time I update the config (using version 1.3.6) it keeps telling me that I should update the firmware to at least 1.4, even though I have updated to 1.4.4 (several times!).