I have ISonics and have sailed sonics for a number of years. Never had a problem. If the supplied fin - (Drake) fits then all my other fins Tectonics, Select, Vector etc, have fitted ok, apart from the usual sanding to make a snug fit(never get Tuttles to be consistent across brands).
Could be the Tectonic fin. Has this been tried in another board?
Also take it to the shop and try it in another Starboard - the boxes should be standard. If it fits ok then it is your board if not its your fin. I have occasionaly had a fin such as a leading edge fin that required me to slightly enlarge the hole but only slightly, I would not be happy with the discrepency you have(if it is the board) and don't see why you should have to start butchering a new board, odds are though I think it is the fin.