Normally I'd assume a server not being on the list means it's locked even to transfers, but if every other server was included, that is odd.

My friend and I have been having the same issue, though - they're attempting to move to Balmung from Diabolos, but when both of us went to the Home World transfer, neither of us could find Balmung listed. Every other server on Crystal and others was there, though - so I really have no idea.