Updates of Evolution can include Unity's physics system changes. Unfortunately, this also means that creatures that have been trained in previous versions of Evolution will most likely behave differently when played back after the update.
When the creatures try to find an optimal movement strategy, they do so in the context of the physics world that they're in.
The simulation saves have to assume that this physics world never changes and can only save the movement strategy of each creature. Because of this, if we now change the physics, the same movement strategy can have a completely different outcome.
Think about what it's like when you have to walk on ice. Walking normally can easily cause you to slip and not make it very far. You have to change the way you walk, slow down and adjust your center of gravity in order to increase your chances of success.
The same thing applies to the creatures in this simulator. Previously simulated creatures will most likely not perform as well, because they are not used to the new physics environment. This is why you might see huge drops in fitness and inaccurate playback of the "Best of Gen." creatures.
Saving your favourite simulation results to the gallery is the best way to ensure that you can always watch them back without changes. The gallery saves a recording of the creature's movement so the playback does not depend on physics at all.
Also read "What is the difference between 'Save to Gallery' and 'Save Simulation'?" for more information on the different saving options in Evolution.
Unity's physics implementation details and when they decide to make changes to them are unfortunately out of my control and given that I have to update Unity from time to time in order to keep Evolution compatible with the latest operating systems, I cannot guarantee that the physics will stay the same forever.