Yeah, running and routing units loose their shield boni (which is what makes phalangitai so strong). If you have a unit of phalangitai running toward you, have your archers fire at it. You'll only get one volley in before they go into formation, but you will kill a huge amount. (Also, when they do that thing where they run, lower spears, run, lower spears... that counts as them in formation at all times.)