doesn't sound good to me; take wheels back to the builder and ask them to verify the wheels being true round and lateral, and same dish on both sides, and tensioning (shouldn't be any the ring too high or low compared to other spokes on the same side)

if they start turning nipples, are they putting tape on the spokes to detect wind-up? more of a concern with the thinner double butted spokes like Sapim Laser

you should watch the verification; if they are true, have them put the wheels on the bike and have them check the side to side offset you notice

wheels that are "finished" and not dished evenly on both sides are a pain in the ass to fix and there is risk that the tensioning will be incorrect; if I had a finished wheel that was not dished correctly by 1 mm I'd loosen all the nipples and start over