Hi,
it could be possible that your own pcb (including the wires) causes the problems. You can try to set the access timings to very relaxed values.
If the at91 also supports the early read/ write you should disable this for test.
Verify that your programm, which accesses the flash, uses a noncached/ nonbuffered area for doing this.
Also be sure that all power lines of the flash chip are connected.
And at least you can try to collect the wires (if possible) to one bundle. Sometimes this helps.


Best regards,
Edi