On a three peice, check to make sure the limbs aren't shifting in the pocket once you put tension on them by bracing. Other than that you could do the string with hanging weights on each end test to make sure of the total bow alignment at rest. That will help you determine true center of the limb tips. Once you have that you can make adjustments from there. It's sounds like though if you are not seeing the alignment shift after adjustment then the limb base may be shifting in the pocket.