if by "turn the sub up" you mean you are just turning up the gain on the amp, then this is likely your issue. Turning up the gain does not mean "make it louder". It is there to tune up and down to give you the best sound for the input given. Since you are on the high inputs from the factory radio, then your gain needs to be set fairly low. If you were using low inputs then you could turn the gain up more. Odds are you will get better results by turning you gain down.