I have found
your Gliese 581 system, and also have found the mistake in it.
The problem with this particular simulation is that you have a milky way there. Not that is not possible, but take a look at the diameter of it. It simply encompasses all the other stars, and because of this all those bodies are strongly influenced by the mass of the whole galaxy. You also locked the stars, but left the planets unlocked, so the stars won't move, but the planets were under the strong milky influence, and drifting away.
To fix this particular scenario I see two ways. The first one, a dirty trick would be to make a static nulled milky way. So first lock the milky way, set the diameter to one sun, and press O to force the disk of dust to spin around the now static milky way, you need to do this to fix the speed of the dust so it wont fly away once you lock the galaxy. After doing that, you can set it's mass to 1 gram, and you can then lock the stars and follow your original idea.
Or you can again set it's diameter to one sun, leave the mass alone on 1 milky way, so it will still influence those stars and they will orbit the galaxy as they are supposed to. Preferably lock the milky way, or hit O to make the other inner bodies including the dust disk to follow it's path. Now go to the stars, fix their orbits around the galaxy, then go to the planets and fix theirs in relation to the stars. This way is cooler but the downside is that the projected paths of the planets will now be drawn in relation to the biggest mass around (the galaxy) and not to the stars they are orbiting.
In short, your milky way, let's say "ball", was too huge and all the other pieces were inside of it. It's gravity was destroying things. Set the center mass where the center is and make it "small", and things should work ok.
Bellow is the same system "fixed". Orbits are all incorrect and stuff, but the systems are stable, with planets orbiting their stars and the stars around the galaxy.
EDIT:
We are influenced directly by only a very small part of the galaxy's content. What happens is that everything in the galaxy is tugging everything close by, and so on, and that makes the whole disk spin around the center, like a huge fabric. Since we can't simulate all the bodies of the milky way so that these 3 systems move the way they should inside the galaxy, we need to sum up all that tugging into one center mass, a gravity blur "tool" if you will, and that will somehow emulate the impossibly complicated gravitational forces that go from the inner part out. Of course it will be 6 billion light years from precision, but at least the stars will orbit the center of the galaxy and mimic the real scenario. The solution then for a "gravity blur tool" is to put the whole mass of the galaxy centered into a small body.