Thanks, I'll treat it as a bug. This is a machine that has been upgraded over many versions, so may have stuff left over from earlier versions.
I've just compared four servers. The two servers that were installed with SME6.0 are both okay - they have only V2 protocol defined. The two servers that were installed initially with SME5.5 both have V1 protocol in them.
Thanks for the help - I'll get a bug raised.