The audio header on the main board nearly always allows you to use a case with switched sockets (which yours are not).
So they supply an outgoing and a return pin for the signals - which is why I presume you have the problem.
With case wiring like this, you have to choose whether to use the front sockets or the rear sockets - you can't have both. You would wire the case wires to the "out" pins after taking off the jumpers.
Not sure about the bass - I've not come across one like that yet.