If you didn't have this problem before, nothing that the shop did should have created it, except maybe replacing the chain. Chain line is built into the system, by the relative positions of the crankset and rear cassette, neither of which get moved in a tube up.

I call your problem "shadowing" because it's comparable to a short person being in the shadow of a taller one if he stands too close when the sun is behind the tall one. You can separate the rings slightly, but run the risk of the chain getting trapped between the rings or riding the top of the inner while leaning on the face of the outer.

If you only get a bit of slight shadowing on the smallest sprocket, living with it is the smartest action. If shadowing is affecting more than one rear sprocket, then a narrower chain, or more chainring separation might make sense.