Are you using any crew mods? Possibly what they changed is reverted by the crew mod as the crew mod may have been using (outdated) vanilla code as a basis. I don't know the specifics of what they fixed though. But the other thing is this. They fixed a source of the duplication... the source they found. Possibly they didn't find the ONLY cause. What would help is this, after your crew duplicate, please provide your starbound.log found in /starbound/storage/ which you can either attach as a file, or copy/paste ideally within both code and spoiler tags. As for the version, that's some small text when you bring up the menu which pops up after hitting <esc> and is also available in your logs.
well the issue stopped happening to me for some reason. The only crew mod I'm using is followers keep up and keep quiet so if it happens again I'll try removing that and/or posting my log