So I thought it might be a race condition of some sort, so I enclosed the
apploopnr checks with an @synchronize, like so:

3636      @synchronized([NSApp class]) {
3637          if (++apploopnr != 1)
3638              {
3639                  emacs_abort ();
3640              }
3641          [NSApp run];
3642          --apploopnr;
3643      }

Sadly, still crashes.
I may have done the synchronize incorrectly, I am not really a cocoa / objc
programmer.