I've noticed some configurations depend on what order the tiles are processed in, so if you swap two tiles around, even if they're the same kind of tile, you can get different results.
Simplest example is two pushers, one behind the other - in one order they'll move in step and stay touching, in the other order they'll separate and be a block apart.
If you run the simulation and then reset, it seems to reset into a consistent order (top to bottom?) so if you move nothing and run it again, that will have a consistent behaviour.