I have created a Circuit diagram and connected the Symbols to their proper Footprins via the assign PCB footprints diagramm. There are three connectors in the PCB. Two 2x5 PinHeader and one 2x30 PinHeader
For the 2x5 I chose the Vertical Version (Conn:02x05_Odd_Even : Connector_PinHeader_2.54mm:PinHeader_2x05_P2.54mm_Vertical) all is fine and dandy.
For the 2x30 I chose the Horizontal version (Conn_02x30_Row_Letter_First : Connector_PinHeader_2.54mm:PinHeader_2x30_P2.54mm_Horizontal)
When loading the Netlist there is a ratsnest to both 2x05 but none what so ever to the 2x30.
Do i have to specify which via is a1?
If your schematic wires are properly connected to the 2x30 connector the small circles around the pins disapear.
Then run an ERC check in Eeschema, does it complain about unconnected pins?
Then, while transfering the netlist to Pcbnew, carefully read all warnings and error messages.
I suspect that the 2x30 pin connector on the PCB is somehow not recognised by Eeschema. You can simply delete it and then when you transfer the netlist to Pcbnew again, it should also import a new 2x30 pin connector from the library.
If it does not do this, then the link to the footprint for the 2x30 pin connector in Eeschema is faulty. You should then choose the right footprint for it before transfering the netlist & components to Pcbnew.
It is a normal process to do this multiple times when schematics evolve. During import in Pcbnew you can even choose if you want to keep or delete unused components during import.
This is because the symbol selected uses pin numbers like a1, a2, … b1, b2, …
The footprint uses 1,2,3 (no matter what order on they are in there will be not a single match resulting in no schematic connection being transferred over to the layout.)
Missing connection can of course be additional problems. But there is as of yet no evidence that this is the case (only if changing the symbol does not resolve the issues could we say anything in that direction with any amount of certainty)