I think I found my problem. Partly due to my own laziness.
I prefer to just type 'rake'. Not 'bundle exec rake'. I do this with my Rails projects and do it with RubyMotion. It makes it easier but you need to sync the version of Rake on all your projects. So today after updating Xcode to the new release from the App Store, I went to one of my RubyMotion to run a test and make sure everything was installed, ran 'rake' and then BOOM
uninitialized constant MK (NameError)
(I use Motion-Kit, MK is the namespace module)
Which means that my gems are not getting compiled. And gives me that sinking feeling in my gut because I haven't been able to figure this out, ever.
To prevent a long story from getting even longer, I remembered that I had a update to the Rake gem last week. So when I did 'rake ---version' and 'bundle | grep rake' they were different versions. Doing "bundle update rake' brought my Gemfile.lock version Rake in line with my default version and then my Motion-Kit gem compiled properly.
So if your Gems are not compiling, check what version of Rake is in your Gemfile.lock versus your command line version or try re-executing your build with 'bundle exec rake'
Hope this saves someone the hours it has cost me.