Gui vs. Quartus command-line exectuables

Not sure of the exact answer and please file an SR, as it seems like a problem that the fitter doesn't detect this. (I'm guessing this flow isn't tested, as command line users tend to stay in command line).

That being said, I am guessing you're running the fitter from the Task Manager on the left. I close this down and never use it, as it tries to be smart and figure out if something needs to be re-run. If you go to Processing -> Start -> Fitter, there are no "smarts" and it runs the fitter, just like if you ran it from a script. If there was a problem with synthesis and the fitter can't be run, you get an error and it says to re-run synthesis, but if you already have it should just work.