In the attached example I would like to align the main labels (S1, S2 and A) centered. In the concerning dialog in engrave options stave labels I can’t find a solution. 
Play with the indent until it fits your requirements. Oh, and you didn’t attach anything 
Ah! I misunderstood the question. I’d need to be in front of a computer to work this one out - hopefully someone else will chip in…
I suspect the problem is that you pressed Enter when you edited the “S1” and “S2” names, so the name is actually “S1 followed by a blank line”.
The “feature” which makes the cursor disappear at the end of the line when you are editing the names makes this hard to spot, especially if you expect “enter” is going to terminate the operation, but it doesn’t.
Thanks, Rob, for the idea. I’ll try it out now and come back to you.
I tried it out. But unfortunately this isn’t the solution.
Well, this is a bit of a cheat, but Setup Mode—click on the instrument and Edit Names. Select the short name and use the vertical offset to nudge it downwards until it works.
I don’t like the thought of doing it this way, but it should work.
Attach the score here, or a cut down version that still has the problem. Somebody will be able to figure it out.