Yeah, I think if you check the quantity in the database, it will be wrong too so just making the Add To Cart show up wouldn't fix it. At least I wouldn't think so. The wrong values are getting written from the BO to the database. I think because Store Manager connects directly to the database (and I assume PrestaTools does too) it writes the correct values directly to the database which is why they worked.
That was about as far as I could ever figure out what was going on.