this may be a silly recommendation so my apologies if it is inappropriate, but I had recently constructed a custom board which also shares the same external memory hierarchy as the DK (so we should have the same SDRAM chips). After debugging my board to full functionality, I would recommend that you test to be sure that every pin is soldered down well on both the SDRAM chips as well as the AT91. Although it is a long shot, it sounds as though "possibly" you have some address pin not making good contact, thus some addresses (which do not set the unconnected pin high) will write correctly, while others result in odd/unexpected placement of data even though the chip is otherwise working OK. I would not expect that the use of separate PCBs to introduce a problem, as long as the ribbon cable is not too long to produce timing issues with the 60MHz SDCK and you have a common ground between the boards.
In my experience, there is always one or two pins that "looked" like they made a good connection, yet when performing a continuity test with my trusty multimeter I would discover the connect was not made. This entire message is of course assuming you hand-soldered your custom board, and that you have not yet actually tested pin-by-pin the connectivity. It may be a pain, but it is worth it if it gets your design working

Hope this helps,
Conger