Ok, so by comparing my persistence file to a fresh version I managed to effect a fix by changing the 'state' in each of the Docking Port 'MODULE' sections. One must be Docked (docker) and one must be Docked (dockee)
MODULE
{
name = ModuleDockingNode
isEnabled = True
crossfeed = True
stagingEnabled = False
state = Docked (docker)
MODULE
{
name = ModuleDockingNode
isEnabled = True
crossfeed = True
stagingEnabled = False
state = Docked (dockee)
