Vader wins round 1. Usually Barry is such a nice/goofy guy, that he spends his fights darting around(at speeds normal people can hit him), hitting them(at velocities that normal people can easily withstand) and wondering why he's not winning. At that level, with Rebels feats and all 6 movies, Vader will murder him.
Flash wins round 2. With CIS/PIS off, he'll probably just speedblitz Vader and rip his helmet off, screw with his circuits, and just hit him at Mach 3.