Rev. C boards from Element14
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First, thanks for this incredibly useful tool - I use it all the time! I recently got some Rev. C boards from Element14 and the tool stopped working. It appears to be a change in the U-Boot.img on the EMMC. If you are having this problem and save-emmc isn't loading automatically when you insert the SD card you may be able to work around it by mounting the card and creating a directory called 'dtbs' and copying the file named am335x-boneblack.dtb into that directory.
More detail can be found here: http://www.element14.com/community/message/136214/l/re-bbb-s2-user-boot-button-not-working-on-element14-board
I learned a lot about this process here: https://www.marshut.net/irqnmm/changing-bbb-boot-default-from-emmc-to-usd.html
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.