No, because cd sound fine does not mean that all is in phase. You simple may have the cartridge pins connection on one side reversed. I would make sure this is correct. Double, triple check your cartridge connections.
The connections on s should be as such
Red White
Green Blue
when looking from the front of the cartridge/table to the back.
The connections on s should be as such
Red White
Green Blue
when looking from the front of the cartridge/table to the back.

