difference I noticed is Linux is detecting the device id of 103Ah and the eeprom has a device id of 1039h (this value should be correct).
This is written in some datasheet (IMHO ICH4) It means that the ROM values were not used. I tried to help you so I read some datahsets but without any luck to ROMchip. Maybe you can try to scan original bios for same values as there are in the EEPROM. Maybe there is somewhere a pointer to them.
Rudolf