To me, the Run feat is something an athletic type such as a modern day track runner or football running back would take. Thus, wearing heavy armor would negate this feat.
I'd allow an alternate feat, Armored Run, which would enable, say, an experienced knight or man-at-arms to "run" in his armor. With this feat, he could spend a full round action moving at x4, which in heavy armor would be 80' per round. Even with this feat, however, I'd only allow someone to run in heavy armor for a number of rounds equal to half his Constitution; with a DC 12 check for running on the round after; and increasing that check by 2, cumulative, for each round of running thereafter.