Okay, so obviously this workflow hasn't been updated for Alfred 3 yet. It's working (mostly) for me, but I chose to "migrate settings" when updating to A3, but I'm guessing you didn't do this?
Anyway, you might be able to fix it by manually updating the preferences location. Reveal the workflow in Finder, go into "scripts" and open "first_run_check.sh" and "includes.sh" in a text editor. Change any references to "Alfred 2" to "Alfred 3". Then "nuke" the workflow by running "timer nuke" and see how it goes after that.
As I said, it's currently working for me, so I can't test that procedure properly, but hopefully you can figure your way through it. If not, you'll probably have to wait until I update it for Alfred 3. Which probably won't be for a little while.
Good luck.