First - make sure you're applying enough force when tightening the cups - Use a torque wrench. Otherwise, I seem to remember that the cups allow a few mm of left/right adjustment of the chainline by screwing the cups more/less into the bbshell relative to each other; eg non-drive cup in further, drive side less far = chainline further out, and visa-versa. If you're certain you're torquing the cups in hard enough, then could this account for what you're finding?
First - make sure you're applying enough force when tightening the cups - Use a torque wrench. Otherwise, I seem to remember that the cups allow a few mm of left/right adjustment of the chainline by screwing the cups more/less into the bbshell relative to each other; eg non-drive cup in further, drive side less far = chainline further out, and visa-versa. If you're certain you're torquing the cups in hard enough, then could this account for what you're finding?