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The board I've worked on evolved in a similar way. Pretty much pin-for-pin compatible, except all the power supply stuff.
I guess you should double check all the supplies to the NAND (presumably a 3.3V rather than 1.8V). I've had to add support in AT91Boot for the ST and Micron NAND's we're using. If a BGA part you might want to probe the circuit (perhaps on the solder sample, look for opens, short, unconnected nets), and xray to double check the soldering. BGA's can be very problematic with via-in-pad, non-uniform fill, or solder-mask shrink. Check the pad voltages on a board without the NAND populated. Revisit any DRC failures for the schematic, revisit the nets in case you've created any unconnected islands, powers, and grounds.
Check power supply sequencing, and resets.
The fact ROMBoot can't use the part suggests the problem is pretty fundamental, rather than some random flakiness.
For the 9260 and 9G20's I've written diagnostic apps I can run/debug in SRAM or SDRAM from within Keil, and those can either test the NAND array or SDRAM.
You could write some code to read the NAND array, try some commands, check there are no stuck-at problems with the data bus or addressing.
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