Google Image has multiple images of how a 3 way switch should work.

I don't know exactly what the problem is with your system but I wonder if you have actual 3 way switches?  (I know nothing but what I read regarding electrical)

Check out this link for diagrams and instructions for a 3 way switch.  What the switch looks like and ways to wire.

http://images.google.com/search?tbm=isch&hl=en&source=hp&biw=1184&bih=571&q=3+way+switch+wiring&gbv=2&oq=3+way+s&aq=1&aqi=g10&aql=&gs_sm=c&gs_upl=2163l6923l0l9783l9l9l1l0l0l0l244l1468l0.4.4l8l0

TURN OFF POWER BEFORE WORKING AND CHECK WITH MULTIMETER TO BE SURE POWER IS OFF.