One thing I'd be curious about is trying another type of store - home depot or lowes perhaps if they allow dogs where you are. I'm wondering if there is something they used on the floors in these places that causes her apprehension. Maybe they have changed their cleaning fluids? Or maybe it had been freshly cleaned just before you went?
Other than that, all I could say is just walk around the area that she's comfortable with, ask for crossing the threshold after all that, leave if she doesn't want to. Do this several different times.
That's all I got. That and try to stay matter of fact about the whole thing.