I can confirm that 13.1.1.3 has NOT fixed this.
Still having issues collecting a project in CC 2014 (13.1.1.3) on Mac OS 10.9.5
However, the "don't touch the mouse" thing above does work. As soon as I move the mouse, the collect fails with the After Effects warning: The File ... 'could not be found' etc... even though there is no missing footage.
Fix this Adobe. People have to continue to work while projects are collecting. Can't sit here not moving my mouse when a large project collects