My bet is that your volume pots are wired backwards. You have likely wired them up like you would the volume pots on a Les Paul. You need to wire them up like you would on a Jazz Bass. This will allow the volume pots to be used to blend the sound of the pickups. It's just 2 wire on each pot that need to be reversed.
Here is a drawing of a Les Paul system.
And here is the same system that is corrected to allow the volume pots to work independently
The yellow solder points in the second drawing are the ones that need to be swapped.