I had the same problem, but found a solution that worked.
I have my one store location, and a few app locations from different POD and dropshipper apps. All locations were in one shipping profile at the same flat rate.
Like everyone else, whenever items were being added from more than one location, it would always double the postage, but I noticed it never went more than double; even if I had items from 3 or more app locations.
That was how I worked out the solution.
I removed my store location from the shipping profile, and created a new profile for it with a new name. I then set the zones and rates the same as it was before.
Now, there is only ever 1 charge added for postage no matter how many locations items are being sent from.