I had a similar problem with a large .rtf file-- it had a bunch of photos. I removed the photos and resaved the file. Deleted it from the reader and then added it again. Worked fine after that. The problem seemed to be both the photos and the overall file size.
The "do not disconnect" message always stays on the screen until you press the eject button in the connect software or close the connect software. It isn't really saying a transfer is in progress, just warning you not to disconnect if you are.
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