When you're working on a rocket and want to make a change to an upper stage, often times you'll grab the interstage below where you're working and remove the lower stage to get a clearer view of your work, then when you're done you reattach the lower stage. The game however can't seem to remember the staging order and instead puts your parachutes and upper stage engines all in the 1st stage and randomizes everything else. I don't know what algorithm the game uses to auto-stage but its very broken. It should remember the order of staging and assume that if a part is being added to the bottom of the rocket, it probably needs to go earlier in the staging order.

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