Identical seeds not spawning identically

I restarted a world I had started earlier in the beta (pre copper at least) as I wanted to do something differently.  Its features are not spawning the same sadly.  The mineshaft I recall is in the exact same spot and to cursory exploration is the same basic design, but in my first version, it had a zombie dungeon down one hallway that simply isn't there anymore.  I thought large features like this always spawned in the same locations?