| Lower action can be easier to play but, especially if you tend to pull hard with your right hand, can create noise and rattle. Generally speaking, the instrument does not "speak" as well and the tone is not as good as it can be. Conversely, higher action can be a little more difficult to play but the improvement in tone is often worth the energy you have to expend to adjust your playing to this kind of set-up. BTW, no matter what you do to your action it only takes a few weeks of playing to adjust your technique.
This question is difficult to diagnose without seeing the instrument. First thought is that if you took the instrument to a pro for a setup take it back and have them fix it. If you did it yourself there are a series of questions you need to ask and corresponding procedures to follow. It is much easier to help you if you can give us some data.
An average set up on an average bass guitar sets the string height ~5/64" and 6/64" treble and bass respectively with ~.010-.012" of relief measured at the twelfth fret. Neck relief is the amount of curvature in the neck. The easy way to measure this is with a precision ground straight edge and feeler gauges. Failing that, fret the E string at the first and last frets and have an accomplice push the feeler gauges under the string at the twelfth fret. The gauge that just slides under without disturbing the string is the correct measurement.
Here are somethings that you can look at with out measuring:
1. Check the saddles. Do the saddle heights follow the radius of the fingerboard? If not, make it so.
2. Check the saddles. Are the saddles parallel to the bridge/top of the guitar? If not, make it so.
3. Check the saddles. Are the saddle heights progressively higher as they march from the thinnest string to the thickest? If not, you know what to do.
4. Did you adjust the truss rod? If so, what did you do? You may have to undo it.
Since it's killing me I gotta ask: If you liked the way it was set up why did you let someone talk you into changing it? | 
