Dear John
Seems that you have assigned some reference variant in your costing variant. Please check the settings of that reference variance as whether it is allowing price updates or not and the transfer control is same as that in your costing variant etc.
Secondly you try to cost your material using CK40N using correct costing variant . Sounds weird but take a try.
Have you checked the customs message ZK33 as suggested by Ajay Sir? Many hints may be hidden there I strongly believe.
Regards
Rajneesh Saxena