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I have the same issue. It's a glitch in the way Calibre works.
Calibre won't let you configure which directories to scan for any MTP device, unless that device is plugged in.
When you plug in the device, Calibre immediately kicks off a full scan of the device. This may take more than an hour.
While that full scan is running, you can't configure Calibre.
Catch-22!
So, the only way I can see to do this is:
1. Plug in the device
2. Calibre will detect it and kick off a full device scan job.
3. Be patient and let the job complete (minutes to hours).
4. When the job completes, leave the device plugged in.
5. Use Configure, Plugins, Device, MTP to set which directories to scan
Once you've done the above the first time, it should be fast the next time.
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