I had exactly the same issue on Vera after upgrading my Gateway to 2.3.0.
After upgrading the Gateway I had to add each node back individually. Four of my nodes had manual Node_IDs assigned and one had auto Node_ID. As it happened I added Nodes 1 and 2 first which were manual and then added the auto node. It automatically assigned node 3 as the next available node.
I then added node 4 (manual) successfully but Node 3 would only add one of its child nodes.
The problem was that the auto node had added Child ids of 1 to 4. When I added the manual node 3, it correctly added child id 0 but could not add the second child as child 1 had already been allocated by the auto node.
I couldn't find any error messages to indicate the problem.
I eventually found this LUA code which showed all the devices with the node and child ids that had been assigned.
I deleted the auto node, changed the sketch to set the node manually and re-added it. Deleted node 3 and re-added and everything was fine.
I realise this was for a Vera system, but the real problem was the order of adding nodes and probably more importantly mixing nodes with manual and auto node assignments in the same mesh.
I will be using manual node assignment for all nodes going forward!