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I always wait for the eject to actually happen, and I always use the eject device from within Calibre or the system tray if Calibre isn't running. It's never happened on the older Glo with firmware 2.4.0 that I plug in and out much more frequently, so I suspect it's more to do with the newer firmware than anything.
I have noticed though the new reader with only 55 books on it is slower than the older reader with over 400 books on it. And those 55 books are also on the older reader, so it's unlikely it's caused by a badly formatted epub. Possibly it does need even more time after an eject, I'll try waiting even longer after ejecting the new firmware and see if it happens again.
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