Rev. C boards from Element14
Fragment of a discussion from Talk:BeagleBone Black Extracting eMMC contents
Interesting, I just got the Element 14 Rev C board and didn't see this problem. I did have to use the barrel jack though, and had the other issues I mentioned.
I think in this case you are using the S2 button to boot completely off the SD card and thereby getting a consistent U-Boot image. I'm just sticking the card in an powering up the board, which relies on the U-Boot image loaded on the eMMC. There's not a strong reason to do that except that booting without S2 is simpler and does not require using the barrel jack.