[Q] Windows wants to format the internal disk on my nook

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I have returned my nook color to stock by flashing "nook-complete-restore-1.0.1.zip" from within the clockwork recovery (on the external sd card). The nook runs ok now, but when I connect the USB cable, windows tells me I need to format the disk because the volume does not contain a recognized file system. Windows sees the other partition as an empty removable disk. How do I get back to having a valid file system on the internal sd card? I have reflashed the 1.0.1 image multiple times, thinking it would format the internal disk properly. I have also tried to install the 1.1.0 update but it wouldn't take. Lastly, I have flashed repartition-boot-with-stock.zip but that didn't help windows recognize the internal partitions.

I am at a lost of what to try next. Any help is appreciated.