When is it that it happens ? at launch of application or when opening with Xcode ?
Because I've not the nib that give problem, I can't give precise reason.
So I put general infos there. They are three features for nib files
1 nib Bundle editable and compilable. Contains files keyedobjects.nib, designable.nib ***
2 nib Bundle not editable and not loadable, called striped. Contains only keyedobjects.nib
3 nib only file. (not loadable) it's the file keyedobjects.nib with name changed in MainMenu.nib
These three features are usable by the system but only the first is usable by Xcode or ibtool..
Since 10.10.6 Xcode uses mainly xib files for edition of GUI. ibtool is the utility for xib and nib.
In terminal type: man ibtool
*** Be careful, structure of editable nibs has changed with MacOSX 10.10.6. (or 10.10.5, I forgot !!)
*** Very old editable nibs contained 3 files: objects.nib, info.nib and classes.nib
I don't know if my answer is sufficient ?
Miguel