Something interesting I have noticed a couple of times when booting my nook ST is that the SD card found/mounted icon flashes after the home screen has already rendered on the screen. So my guess is as someone mentioned earlier, the issue is the mount order on booting. It sounds like the OS is reading in to memory and/or checking shelf content and the file pointers before it mounts the micro SD card slot. So it is seeing broken pointers and removing the content in some manner from the shelves and then mounting the micro SD card.
That is my guess anyway. Seems stupid on a lot of levels as it shouldn't be checking any file pointer until you either pull up your library and/or go to the shelf display.
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