@RobertCNelson
My guess at this point is that the kernel is trying to fix the filesystem. If I power the device off, without using the reboot command and within 15 seconds of the device write I am able to get SPL to load u-boot with no issues. I have also found that if I completely crash the kernel this will work as well, upon a manual reboot it works as well.
To crash the kernel
echo 1 > /proc/sys/kernel/sysrq
echo c > /proc/sysrq-trigger
flashing commands.
sudo dd if=./MLO of=/dev/mmcblk0 count=2 seek=1 bs=128k conv=fdatasync,notrunc
sudo dd if=./u-boot.img of=/dev/mmcblk0 count=4 seek=1 bs=384k conv=notrunc,fdatasync
Thanks again for your help during this project.