So that suggests the stops on the rear derailier were not set right.
I would have told you too return it but as you have had work done to it I am not sure that is an option now.
I did phone them up the day after i bought it telling them about my concerns that i thought i should've bought the Specialised triple chainset they had. They reasurred me that the bike was lighter than the Specialised,had a better spec and was a better bike. I suppose they wanted shut of it, but the Specialised cost more than the bike i ended up with, so their profit margin wasn't the issue. They saw me coming, some might say!
I should've taken it back there and then and ignored their waffle but i didn't know at the time how things would turn out. The bike has a Tiagra front derailleur, a 105 rear derailleur and i've forgotten the make of the chainset(It's not Shirmano) and i can't look at it to tell you as it's in my mates bike shed waiting repair.