@patchymama: The way calibre device detection works is that it waits for the OS to detect and mount the device. But it will only wait for a fixed amount of time, before giving up. Probably something on your system is causing the OS to be very slow when auto mounting the device, which in turn causes calibre to give up. On the other hand if you connect the device form before, there's no such constraint.
@pthwaite: That's weird, I can't think of anything taht could cause that. There certainly haven't been any changes to the driver subsystem since 0.6.20
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