Oops, sorry, I forgot about that post.
I've found the problem, I've made a fixed blueprint for you.
This occurs because you have a capsule, but also a probe on your first stage. The problem is that the probe was the main device. So when you separate the first stage, you keep this one under control. But for the second stage, the game will tend to prioritize the part that was connected with the separator
That's most likely a bug, but we have to do with it.
I just made sure that your main controlling device would be the capsule. That way, you won't have that problem again.
In terms of priority, the main controlling unit will be the first placed. Moving a controlling unit will place it at the last place in the order of priority.
So if you want to make sure that a controlling unit is the main one, move all the others, and put them in place again. The only one untouched will be the controlling unit.