ALTLVDS_RX behavior on Quartus II 13.1 and Quartus 14.0

Whether someone responds or not, please file a Service Request with Altera. There were a number of changes in Q14.0, although they should mainly be GUI related and not how the underlying IP works. If you can submit the original megafunction, as well as something to show the original alignment and what you're seeing now, that would help? (I thought cameralink did some strange serdes, i.e. something like 7:1, but don't remember. Regardless, it shouldn't change.)