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Originally Posted by JvdW
J
Disconnected throught the icon next to the library, took the usb cable out of the Reader and started timing when the text 'usb connected' disappeared--> 2:20
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This is completely consistent with the Sony and calibre fighting over dates.
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Closed Calibre, plugged my reader in, waited until the windows dialog appeared asking what todo with the new drive, close that window, ejected the reader and took it of the usb cable, started timing when 'usb connected' disappeared--> 17 secs 
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And this is what it should be
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Just a wild guess, but I think people should tell whether they are running a plain reader or a reader with for example PRS+. I'm running PRS+ 1.1.3 WITH a date setting of MM-DD-YY which is NOT the DEFAULT and might explain why it takes so long.
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An excellent thought. Yes, it would cause the problems.
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Is ther anything I can do to help debug this?
For example take a snapshot of the files modified with and without Calibre active?
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The best debug information would be a copy of media.xml before and after calibre connects to the device. It is in database/cache/media.xml. Connect the device, make a copy of the file, start calibre and let it connect, stop calibre, and make another copy of the file. (I know that you know how to do this. I am just being compulsive.
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If there is nothing in the files that you mind people seeing, create a ticket with both files attached. If you would rather keep them private, PM me and I will give you my email address.