The change in checksums is the result of small changes in the MAX PLUS II or Quartus synthesis algorithms caused by a change in design hierarchy. However, both programming/configuration files are still correct, and either file can be used to program/configure the device.
For example, you may see a different checksum for a programming/configuration file if you take a lower level design, create a symbol for it, and instantiate that symbol in an upper level design file where you only connect the inputs and outputs to pins (i.e., you do not add any additional logic). Adding a "wrapper" to a design file can alter the resulting programming/configuration file such that the checksum will change.