It's all about exhaust velocity. Okay, at 2 rpms there are minimal exhaust gases, so let's say you have like a 3" exhaust piping and your stock was 1.5". The velocity of the exhaust gases exiting the car on your stock piping will be faster then the 3" piping at low rpm, therefore losing torque. The reason you gain more top end horsepower is that let's say you're at 11 rpm or so . Okay now, on your 1.5" stock piping, the exhaust gases are more congested in the piping and can't be released as quick as a 3" exhuast piping would.
Hope this helps.