This means that you whatever you're loading, is not the same as how it was saved.
This could be because of the following:
-Using a different SVN version of the engine
-Files were modified
-Running files in different order
For the latter, "zdoom.exe -file AEoD.pk3 AEoDdat.pk3" is not the same as "zdoom.exe -file AEoDdat.pk3 AEoD.pk3" for save-load purposes. And if you're running something else with aeod, that one adds to the equation