I've run up against a similar problem to the one Peter mentions that motivated this patch (in my case, JFFS2/NAND ECC compatibility issue between Linux and u-boot on a Freescale MPC8308 based target.)
I've already taken a look at the NAND driver code being used by both u-boot and Linux, and at least by inspection both seem to be using the same ECC setup/strategy. I was wondering if Peter could comment here a little more on the nature of the problem he experienced and the eventual solution?
thanks much,
--FritzM.