Sorry, calibre is not doing anything that could affect this. All it is doing is putting books on the device ready for reading. The device then processes them into it's library so that you can read them. It is more likely that the problem is related to what you were doing when the device went to sleep. Does the light stay on when you are reading? On the home screen? Using a sleep cover, the power button or timing out? I haven't noticed the problem with any of my devices, so can't comment. I have noticed that the light is taking longer to turn off, and fades out. This is only a few seconds longer, but if I close the cover and open it again, the light will still be on.
If you want to prove that it is calibre doing this, then don't use calibre. Use calibre save-to-disk to save some books somewhere on the PC. Close calibre, connect the device and copy the books to the device. Eject the device and see what happens. I'll be extremely surprised if there is a difference in behaviour.
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