Problem The problem I'm having was caused by the following action: When I had BBB connected to my PC (using USB cable), I accidentally formatted the ~92 MB partion that contained the getting started files.
Because of this, each time I apply power to BBB, the USB LEDs do not light up. It only works when I have the Angstrom image on an external microSD card.
What I've tried I thought that this was caused because the eMMC is corrupt and for some reason is not bootable. So, I tried to boot from the external microSD card (that has the newest image running) and to use dd command where if was equal to the current microSD card and of to the target microSD card (built in on the board).
When I restarted the BBB, I looks like dd was successful (when I executed it, it told me that everything was successful). Now, there is one partition with the GettingStarted files and another with the Linux kernel.
Question Despite this, it's not possible to boot from the internal microSD card. Does anyone know how this can be solved? Is there something to do with the boot order?
To force a boot from SD you need to remove power from the board completely, hold down S2 and then re-apply power. Keep holding the button until the four leds start turning on. You have to do this at power on, and once you've done it the board will continue to boot from SD on a reboot or reset, only removing power will change the behaviour. You could also move R68 to R93 if you want to make the board boot from SD by default.
Also note the boot sequence in the table on page 6 of the schematics, by default if MLO can't be found on the eMMC, it'll look for it on the SD card. So deleting MLO normally causes the board to boot from SD if the appropriate files are present.