Description
Starting with the Quartus II software version 12.1, SRAM Object Files (.sof) include debug file packets that contain timestamps. Debugging tools such as the External Memory Interface Toolkit or System Console read information from the .sof. Because the .sof file contains timestamps, you will see different MD5 checksums for each compilation.
Resolution
To ensure the designs are identical, perform an MD5 checksum or diff on the Programmer Object File (.pof) or the Raw Binary File (.rbf) which does not contain timestamp info.