I came across something similar way back.. the two things I missed were:
- ensuring the flexbus mask was large enough (ours was set to only allow 32MB at the time)
- lowering the base address from FC000000 down to F8000000 to allow for the 64MB to sit comfortably at the upper end of memory.
Once those two steps were confirmed, the kernel stopped giving us hassles about the 64MB flash.
I have no idea if it's at all relevant but I thought I throw it out there anyways.
Good luck!