This is the current expected behavior from u-boot for omap3.

By default, u-boot-omap3 is compiled to support writing the environment
at NAND (addr 0x00260000), together with a default environment, but only
loads the default one (that searches for boot.scr) when your NAND
environment is empty. This allows user customizations at the boot
loader.

You can easily notice if you're using your custom environment or the default 
one by a warning from u-boot:
*** Warning - bad CRC or NAND, using default environment

So we have to possibilities to fix this issue:
1 - Document about possible issues regarding setting your own u-boot 
environment. You can get back to defaults by getting into u-boot prompt and 
giving "nand erase 260000 20000";
2 - Change u-boot to disallow personal environment customization. Easy fix, 
good for the distribution but we remove a feature from u-boot.

What do you think?

-- 
u-boot loaded from SD should look to SD for boot.scr instead of using nand 
settings.
https://bugs.launchpad.net/bugs/613866
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