I'm not 100% sure I understand the question... I'd probably need pics to make a call on it. If you're judging the cranks position on the damper's markings that may be the issue right there... the rubber in the damper dries out and warps over time allowing the outer sleeve to slip putting the marking out of alignment. If its ony one or two millimeters off I wouldn't sweat it as long as the crank was really at 0 when you zeroed out the cam gears. If you judged by the damper, just pull the #1 spark plug and rotate the crank manually until the chopstick stops moving upward... now you're at TDC.
A couple degrees won't keep it from running and timing's easy to redo if things don't feel right.... If I'm misunderstanding what you're dilemma is then please post some pictures.