Agreed. The nut should only be high enough so that when you press down a string on the 3rd fret, it clears the 1st fret by about .010", anything higher and you run the risk of throwing off your intonation at the lower frets. The nut has very little bearing on the tone of the bass after you stop playing open strings.
What kind of bass are you playing? How long has it been since it's had a setup? Have the notes on the lower frets always been softer or has the problem arisen recently?
Softer-sounding notes can be caused by several things: dead spots in the fretboard, a soft neck, truss rod adjustments, etc. If you can give a little more information we can probably help out with the problem a little more. The forum is also no substitute for a good repair technician, you might want to take it in to someone who can give you a professional opinion.