I agree with Nuguy that no jumpers are needed and that the decrease in bass is probably related to the new cables.
You can try a couple of things before giving up on the cables. One thing would be to invert the bass and midrange legs of the cables to see if that makes a difference. In other words run the "tweeter" wires to the bass section and the "bass" wires to the mid/tweet section.
Another thing to try would be different interconnects between your components. Start with the pair between the preamp and power amp and see what differences you notice.
Trial and error is the name of this cable game. Unless you just want to cut your losses and go back to your previous cables, why not do a bit of experimenting to see what results you can achieve?