Storyboard violations are suddenly all irrelevant

I am using XCode 6.4. I have a pretty large storyboard and sometimes when I open it, a lot of force warnings pop up saying that I have the wrong views without touching anything. Everything was fine before and the clumsy views are in every view controller. I add most of the constraints manually.

Any ideas what I might be doing wrong, or why all of a sudden everything is moving?

EDIT

I pull from the repo, open XCode and then all the warnings appear. If I am git status

, the storyboard has changed. The difference between the versions is the attribute systemVersion

on the storyboard. This change probably happens automatically when someone else with a different configuration opens the project and then commits the changes. This (long) question is related: Xcode modifies unmodified storyboard and XIB files . However my problem is not the attribute class

butsystemVersion