Rear caliper pins

[Motenmarc]

I have a 2011 Altima 2.5 SL. I recently did the break pads and rotors on my car. All went well except for the left rear. My problem is the new pad on the outside is not meeting the rotor completely. The surface making contact is only about a 1/2 inch. I took everything apart and checked the installation again. Still the same. My caliper bolts slide like they should, I greased the pins also. Here is my question: The rear caliper bolts are different. One has a small rubber piece on the bottom of the pin and the other does not(I am not talking about the boot). Which location does this bolt go in, top or bottom? Could this be my problem? My old rotors and pads wore perfectly. Any help would be greatly appreciated.