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I am having the same issue using a 4Gb card, which worked on builds prior to 1/21/11. I used the tools above to long format as FAT32, but still get the "Waiting for SD card" message over and over.

If I load andboot files to the stock 512mb card, Android boots no problem. I don't understand why my 4Gb no longer works, even though WM uses it just fine.

Any other ideas?