I know this may be a long shot but it may just be a shimming issue. When your engine is cold the metal has shrunk several thousandths of an inch. which may be causing it to just barley touch the flywheel teeth. once warm the parts expand and touch the flywheel just enough to make good contact. I had a very similar problem but one of my bolts backed out and the starter pulled away from the flywheel just enough to make a horrible grinding noise. If you have to many shims between the starter and flywheel this could happen.