@JWalkerMR: I believe what is happening is that Windows is taking longer to mount the external card than the internal storage. Calibre is detecting the device, but the card isn't ready so calibre doesn't see it. When you connect the device when calibre isn't running, the main storage and the card are ready by the time calibre is started and sees the device.
I'm not sure if there is a better solution than connecting the device before starting calibre. Otherwise, there would need to be more delay added to detect the card. I'm not sure if that is a good idea.
Also, the extended driver and utilities plugin will have no affect on this. The device detection is is core calibre code. The KoboTouch driver is what defines the device. The extended driver adds some function to the main driver without changing the detection. The utilities plugin just adds some extra function.
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