Hi Peter, was this cloned server a domain member server? And when cloned, was sysprep run against it to replace the unique ID?
Have you dropped and re-added the server from within SSMS? (Assuming that's how you are connecting to it.)
Sounds like you got the server name straightened out. Did you use
sp_dropserver 'old server name'
sp_addserver 'new server name', 'local'
As for your current maintenance plan confusion, when you query msdb..sysmaintplan_plans what results do you get against each server? Here is an unsophisticated script to delete maintenance plans but better be sure what server you are pointing at before doing this.
Declare @PlanID uniqueidentifier
set @PlanID = (select top 1 ID from msdb..sysmaintplan_plans)
delete from msdb..sysmaintplan_log where plan_id = @PlanID
delete from msdb..sysmaintplan_subplans where plan_id = @PlanID
delete from msdb..sysmaintplan_plans where id = @PlanID