Heres some ideas.
1-Take the door panel off and visually inspect both speakers for water damage, door speakers live in a humid environment and paper cones can warp after absorbing moisture.
2-Press gently and evenly on the woofer cone and listen for any grinding sounds coming from the voice coil to see if any dirt has gotten into the voice coil gap.
3-Check your polarity
4-Check it again
5-Swap the right and left speakers and see if the problem switches sides, if it does, replace the offending speaker if covered under warranty, if not, buy new speakers. If the missing volume still exists on the passenger side after swapping the speakers this means the speakers are not the problem assuming that wire gauge and length is approximately the same size.
6-Check your RCA jacks to ensure that they are inserted securely.
At this point the amplifier or the rca outputs on your deck are the next to be inspected. A manufacturing blemish in the amplifier could cause this or a damaged preout on you deck. Go back to your dealer and ask if you could try a different amp to see if that fixes the problem, if thats not it then move on to trying a different deck.
Now if you do all this and still have a problem with the passenger side being quieter, set your car on fire, walk away and start all over.