The old wisdom used to be that you spaced the crankset so that it was centered with the rear cluster, but it seems like this went out the window at some point. It sounds like your crankset may be too far outboard, and that's why the angle causes the chain to contact the chainstay. If there's a lot of clearance between the inner chainring(s) and the chainstay, you might investigate using a shorter bottom bracket next time you service/replace it.