Our 11ft. Island was crooked by 3.5". Before centering, the countertop was flush with all the cabinets, but now it's only flush on one end and not the other. The builder doesn't know why and won't fix it. It's an open floor plan, so from a distance it's very noticeable and looks sloppy. Why after moving, it's no longer flush on one end?

What do you mean by "before centering, the countertop was flush with all the cabinets?" To be flush with all cabinets means top's dimensions exactly match the exterior of the island cabinets, right? This is a bit surprising, as typically an island top is designed to have a 1-inch or more overhang over the face of the cabinets below, and not be flush. So please explain what you mean. But in any event, if the island countertop is not properly aligned with the face of the island cabinets on all four sides with proper overhang it was miscut, and should be redone. There's an old saying in home construction: "measure twice and cut once." It sounds like the countertop was cut without measuring the actual cabinet dimensions, perhaps assuming (incorrectly) that the cabinets would be perfectly square.

Start with reviewing the measurements are proper for the materials used, and investigating if the foundation has settled or shifted. If the fault is the builders and you have PROOF, then the builder is liable for damages or repairs. Get another contractor to do this work, and get an estimate of repair and the cause of damages in WRITING.

Can you post a picture? Not sure how an island could have been installed 3.5" off, that is a tremendous amount over 11 ft.