Did you find a solution for this frustrating issue?
I am running Xcode 8.1 on latest macOS 10.12.1 and experiencing the same issue (Obj-C project), restarts/cleans/anything doesn't help...
I might as well edit my project in VIM because XCode has turned into a dud.
Did you ever find a solution? Having the exact same problem, and restarting Xcode every couple of minutes is extremely annoying.