Altium 18 multi-board design. How to connect 2 PCB's with a pin header?
I would make a footprint on either board with no 3d component installed and ensure the pins match. Multiboard connectors need a special parameter to link properly. Add the following to both connectors "ParameterName: System, ParameterValue: Connector". Then the MBA should find the pins and walk you through the rest. A 3d component shouldn't be required for this to work