What power supply are you using?
If you are running system from nand, than uEnv.txt is taking control. boot.scr and boot.cmd should not be there.
Is your /boot (/dev/nand1)?
nand1 is boot partition with kernel uImage and uEnv.txt and some other files but not boot.scr and boot.cmd
And you have to remove SD card if you want to boot from NAND .. if it's not booting than check BUG/Limitations and proceed with the hint.