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Originally Posted by eschwartz
Configure the device plugin to list EPUB on top, and MOBI as second option. It will send EPUB if available, and fall back on MOBI if EPUB is not available. If neither is available, it will ask you whether you want to convert the non-available books to a device-supported format.
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I did that, and hope that will be the last bit of the puzzle. It's a pity that dialog is only available when the device is plugged in, but I think I can see why it has to work that way.
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If the book is being auto-converted, this is wrong!!! It means you have accidentally set calibre to automatically do that in the future. Go to Preferences ==> Interface ==> Behavior and use the tool to "Reset all disabled confirmation dialogs".
Now you will be prompted, instead of calibre automatically assuming you want them converted. 
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Yeah, I assumed it was wrong. Calibre is well designed, so my first assumption is a failure in my understanding, and not a flaw in Calibre.
I've been using Calibre to build/maintain an eBook library, and do occasional format conversion for a while. I've just started using it to send books to device, as my previous eBook reader was a Palm OS PDA where books got added by manually dropping them on the device SD card in the appropriate directory, and most books on that device are in a format Calibre doesn't support. (I have about 4,000 volumes converted from HTML to the format used by the Plucker offline HTML viewer for PalmOS package. I use FBReader on both Windows/Linux and FBReaderJ on the Android tablet. A big win for FBReader on Windows/Linux is that it views Plucker files, so I can read them on something
other than my old PDA.)
I don't recall ever configuring that behavior in the fist place, but I did the Reset all disabled confirmation dialogs" bit, as well.
Thank you. This may just have fully resolved my problems.
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Dennis