Installing new rotors and pads

I am doing the brakes had come across a problem. I have pushed the caliper cups back with the caliper tool and when I put the new pads in and go to install the caliper it will not fit over the rotor. Now, I have been doing disk brakes for a long time and never came across this problem. The cups will not go back any further, I have tried. It is so close but will not go on like it should. It is a two piston brake caliper. I took the caliper off the car and tried pushing cups back more but they go no farther. What am I doing wrong?