Purdue got the majority of their rushing yards on only 2 plays (1 run by Moore and 1 run by Knox). The bigger issue that Northwestern had in the game was contending with Purdue's "speed guys." They were taking some poor angles.
And take away Larken's big run and NW averaged less than 3 yards a rush. Take away the two Purdue running plays you mention above and PU still average ~4 yards a rush. The issue for NW is the same as it has always been - the defense isn't that good (even though it gets a lot of credit) and they tend to get pushed around on both sides of the ball.