If you connect 2 separate networks, it asks you if you want to merge them. If you say yes, it doesn't actually merge them. Steps to reproduce. Place a 1x10 header layout on a new PCB. connect the first 5 pads as one network. connect the last 5 pads as a different network. connect the middle two pads. Say yes, to merge the networks. Observe that all 10 pads are NOT on the same network. Set Board Outline so you can run auto-router. run auto-router. observer that all 10 pads are not connected.