Thanks for responding. No, unfortunately that doesn't change anything. Still getting the weird behaviour.
I'm still trying to work out if its Alfred or something else causing the problem. Tho it only appears to have started happening in the last 5 days or so.
Using OSX 10.9.1, Alfred 2.1.1, Photoshop CC 14.2, and Default Folder X 4.6.2. (I can disable Default Folder X tho and the problem still occurs, so I dont think its the problem)