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This sounds very much like an issue I had on a Touch; the SD card would not stay mounted in the device. Unfortunately I gave up playing with it (and seemed to be the only person on the beta list who ever saw this).
The symptoms were I would add material on an SD card; it would be scanned and the books would appear in the library. Without my doing anything, I would suddenly see the screen flash, and the content from the SD card disappear.
This also seemed to prevent my Touch from ever entering the sleep state.
Unfortunately, since this mount / unmount cycle happened at the OS level and not the application (Nickel) level, I really doubt that an alternate reading S/W will make any difference.
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