No, it is not strange that replacing the head unit made the system sound better. Every piece of the sound system contributes to its overall quality. Every piece in the chain contributes to the overall distortation relayed to the speakers and an amplifier is going to amplify the signal it receives. If you are sending a crappy, distorted signal to the amp that is what you will get out of your speakers. By replacing the headunit you have replaced one of the weaker links in the chain.