Something weird here. Passive guitar tone controls are only capable of reducing the treble, they can't increase it. With your new arrangement (which I also use), with the volume controls full up the pickups are effectively wired straight to the amp.
Some possibilities: - The volume pots are too low resistance, and are loading the pickups. - If the problem only occurs with the volume pots away from 100%, consider a bypass capacitor (quite a common trick). Yell if you need more data.
Steve
http://www.fivetrees.com