What mode are you using talking about please (-s/-m/-n, -d1/-d2/-d3)? MAMEDiff works quite differently now so I can't explain the reason without knowing what mode your are actually referring to. Resource changes are included in the generated data files but games do not refer to parents or resources for the sake of it now. This is because the behaviour across modes d1/d2/d3 has been made consistent (well, it's one piece of code now rather than two completely different algorithms). In all changes/supplements modes, games are essentially treated as individual ZIPs and cloneof/romof has basically become irrelevant. I don't imagine that you are using rebuildto paths for changes/supplements so I guess that you've been comparing the output of two MAMEDiff versions? I'm interested to know why this affects you. ;)