First of all the amp is not enough for the setup. 938s are 100 watts rms each and your amp output is 40 watts rms each channel. When underpowered, installer increases the gain resulting in clipping and distorted sound.
2nd.. As Madhouse said it could be a polarity issue. Try changing the rear speaker polarrity from negatives to positives and see if the issue is resolved.
Turn off the subwoofer option from headunit as it has 2 rca outputs. Front and rear/sub. Turnoff loudness. Set the hpf off from head unit and adjust it from the amp or set at full on amp and turn it on from head unit. Using filters on HU and amp both causes distortion most if the time.
I would suggest you to visit Entertainment in Wheels in Johar town near Topaz comolex. They are very expert. It could just be the wrong setting or bad wiring. If you need a new amp they have wide range. And the owner do not suggest anything unless its necessary.
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