Solution to Soup Kitchen problem
DO NOT talk to Cue Ball until you have done everything else in the game that you can. If you talk to Cue Ball before you absolutely have to it will cause the glitch. You don't have to talk to anyone or click anything to trigger the cut-scene, you just have to walk around the corner to Emmett.
I have played it through this way several times without a problem after getting stuck the first 2 times I tried it.
I think the bug has something to do with Emmett, and whether or not he's there when you talk to Cue Ball the first time.