There are wacky things going on with the reservation system when on AS ticket stock and upgrading to MCS. It seems to create another copy of the segment in VX's system (with an MCS booking code) and then should delete the AS segment (which is duplicated in VXs system which is why it needs to get deleted). However, this doesn't always happen properly and you may get duplicate segments when you check on VX website. Then you can't check in.