Thanks for the response. Funny how things workout. Only minutes after my post I was able to get another board to boot just fine from eMMC. My main problem was the image (u-boot.imx). It was not good. So, my original attempts at booting it with the fuses set to group 1 (in my previous post) were not successful due to the image, not the fuse settings. I took the wrong path in experimenting with fuse settings rather than fixing my image. After I fixed my image I had no chance of succeeding due to my messing around with the fuse settings. I pulled out another fresh prototype board yesterday, set the fuses as in group 1, let the mfgtool's usb gadget code burn my "good" image into eMMC, and bingo, it booted from eMMC on the next power cycle.
So, for those interested, here's my setup for getting u-boot to boot from eMMC:
Chip: eMMC version 4.5
Vybrid Connection: ESDHC0
Vybrid Fuses: Bank 0, Word 5 = 0x00004070
Bank 0, Word 6 = 0x00000010
U-boot image: Modified for my board from the u-boot-src (7/2013) that ships with the mfgtool. It's original target is the tower board (vf610).
Partitions on eMMC: Not necessary for u-boot, just put the u-boot.imx file at 1k offset from beginning of eMMC main partition.
NOTE: I am not sure if the mfgtool is burning my u-boot image into a boot partition on the eMMC, or the user parition. Given the information in the Vybrid RM and the way the fuses are set, it seems like the eMMC4.3> special boot mode is being used in my case. This leads me to believe that one of the eMMC boot partitions is being used, but I don't think the mfgtool is burning my image into one of the boot partitions. The RM shows a flow chart that seems to end up booting from the user partition if things are not setup properly to boot from a boot partition.