If the muscles don't exist in real life (Like from the toes to the chest) turn the muscle strength down to "0.1" and take out as many non-existent muscles as you can.
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I think I figured out 1 part of the "why doesn't it uses its 4 legs?"
I selected "keep best creatures" and it seems that it really helps to reach more fitness, but prevent new mutations to ever been selected because the parents are already going too fast.
So I reduced the number of muscles like you said, and I'm alternatively keeping the best creatures, and not, at around each 50 - 75 generations, or when I see that the "parents seeds" are not making any interesting new children.
I'm not very far in the generations, so I will continue that for a while and then post a video of the new result.
I may modify the spine I think. I'm thinking about adding a joint in the vertical thorax bone just before the spine, and make a "second spine" like the first one, not connected to the other spine (would make a triangle). I think it could help to reduce the bones getting out of their joints. I could connect the front leg bones to one line and the back legs to the other.