Are you sure that the flashes ever worked? One typical problem is that it seems quite natural to connect the D0 pin of the flash chip to the D0 pin of the data bus, etc. - which is wrong, since for the flash chip D0 is the LSB, but on PowerPC bit 0 is the MSB...
Can you access (read, erase, program) the flashes through a BDM debugger?
I don't know the particular CPU, but along the same lines (learn from my mistakes!):
1) did you hook the flash up in the correct mode (8 vs. 16 bit)
2) did you hook CPU addresses to flash addresses correctly? This will depend on the flash mode setting and the CPU. At least one part I've used (Toshiba TX4925) changes the connections between internal and external address busses based on the programmed width of the chip select - i.e for a 32-bit wide select it will connect the A2 out of the MMU to the external A0, for a 16-bit wide it connects A1 out of the MMU to external A0, etc.
3) In s/w when doing the ID cycle are you writing to the correct address in CPU space to generate the right pattern on the physical lines hooked to the flash to make it recognize the ID commands?
and as a reminder of things one ought to be doing, these are a good set of rules: http://www.debuggingrules.com/debuggingrules.pdf (for more explanation on these check out the book "Debugging" by Dave Agans - no affiliation, yada, yada)