It can be very frustrating when you have a nice new bike with chronic noises and little problems.
However, from you description it is almost definitely a derailleur adjustment problem. Perhaps take the bike to another shop for a second opinion. Tell them exaclty what your problem has been and ask them to get their tallest tech to take it for a spin to help diagnose.
The only other thing I can think of causing it is perhaps the chainline is off... modern bottom brakets usually have spacers to centre the spindle and align the cranks in the frame - perhaps it was assembled wrong at the factory and they got it wrong again when they reassembled with the new frame.
Keep in mind, though, that on a 10 speed bike, using the large chainring and large cog (or second or third largest cogs) is not good for the drivetrain. When I built bikes I would always try to set the chain so it rubs a bit during cross-chaining.
Also: Are you aware that Shimano STI shifters have a 'half click' or 'trim' adjustment on the front shifter? You might be able to get the derailleur to move slightly over if that is what is rubbing... provided the front derailleur is adjusted properly to take advantage of that feature.
Good luck!