Ah, okay, that ditches both of my initial ideas. I thought the 49F040 would have a reset pin, but it doesn't. The 49F001 does. The 49f010 does not. I guess if Atmel made an AT49F004 it would have a reset pin.
So, my last thought...did you tie the WE_ pins high on the adapter? I don't think that the logic board will supply a high signal to the WE_ pins because it doesn't expect a ROM to have them.
Jeff
P.S. Oh, and an "Is it plugged in" kind of idea. Do you have the W1 jumper set for motherboard ROM operation and not for ROM socket operation?