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Originally Posted by PatNY
Oh, so you had that problem too? I thought it might have had something to do with the fact I still use Windows XP, but I wasn't sure. Good to know it was not something unique to me and I likely didn't mess up. 
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It happened to me and I've seen reports of it every so often over at XDA forums. In all cases it was a consequence of having written onto the SD card some particular pre-made bootable software images used for rooting & flashing custom ROMs.
I surmise the problem is caused by difference between GPT partition table format used in Linux (the OS of choice for developers/tinkerers who created these images) and MSDOS partition table format used by Windows XP (the prevalent OS for most of us mortals), and hence only a low-level reformat would restore the card to a state usable by Windows systems/tools.
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Since this corruption of the micro sd card when using the image file doesn't appear to be a unique problem, I would suggest anyone modding their Nooks with the CWM card method to use the alternative option for preparing the card -- the one where you set the first partition as active and then drop the boot files onto the card. That's what I eventually did and it seems easier and more foolproof to me.
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Since my brush with the problem, I have always created my own bootable images as you do.