Three-way switch puzzle
If you look at the screws on the switch (if it is a new switch) there will be two silver screws and one black or gold screw. The silver screws are for the travelers and the black screws are for the line voltage coming in and the load voltage going out.

Start by shutting power off and taking the wires off each switch, separate the wires so they don't touch, then turn power back on and find the wire that is hot. If you don't have a meter you can get a tester at the hardware store. 

Next attach the hot wire to one of the other wires from that switch and test the voltage on the other box. Then attach the hot wire to the other wire and test the voltage at the other box. These will be your travelers.

Cut the power and attach the travelers to the silver screws. This will leave on wire in each box that is your line (source voltage) and load (going to the fixture). Attach those wires to the black screw and you should be good.