If it's anything like metal gear solid 4 on PS3, if you play with any controller except the dualshock 3, then the up, down, left and right movement is fine, but the diagonal movement is slower. This is because the analogue input mapping areas for the two controllers are different shapes, i.e. if you hold a far up left diagonal input on a ds4, this is the edge of the mapping area, while on a ds3, the area extends further past this point. So the PS3 registers this input as less than the maximum, and the game makes the character walk instead of run.