These values differ as MCS linear addressing does not match with the Spartan-3AN page addressing format that iMPACT uses to calculate the checksum read back.
To verify the flash contents, you can use the iMPACT Verify operation, taking care that the assigned MCS file matches the configuration data in the flash.
An alternative is to set the ISF in linear (power of two) addressing mode, which enables the result of readback to be linear and match with the PRM file.