This is happening because the application where the autoresponders are being sent is contained in a center. When an autoresponder is sent from a center, it's going to use the configurations that are set in the Center-Level Options. Go to your center and click "Edit Center-Level Options." Look at "Center-Level Autoresponder Reply To Address" and if you see that it is not configured to override the site-level default, then that explains why the site-level reply-to address is being used. You can specify a reply-to address in the center-level options if you prefer not to use the site-level default.