I took me a while to find the mistake: your look-alike symbol is outdated, and does not match the port definitions (port position) in your EM Model ... which means your schematic port connections are not going to those places that your look-alike shows you!
I took me a while to find the mistake: your look-alike symbol is outdated, and does not match the port definitions (port position) in your EM Model ... which means your schematic port connections are not going to those places that your look-alike shows you!
But you are correct, it is not only the look-alike symbol. Pin/port numbers in layout also do not agree with port numbers shown in EM preview (generated from that exact layout). It seems that EM skips some ports, which means the numbering isn't what you expected.
Looking again, I finally found your mistake: you have changed port ground layer from "implicit" (=ground at infinity) to an explicit drawn ground layer. This means that Momentum will place port ground on that layer, just above/below the port "plus" terminal.
And here comes your mistake: for some ports, there is no metal on that layer that you declared as ground reference layer. Momentum seems to silently (?) discard those ports, which means your port numbering scheme is messed up. See pins 5 and 6 position in layout versus EM preview.
Fix: change the port ground references back to "implicit" for those ports where you have series elements with no ground below. Or second option: place an explicit ground pin at a valid location (on metal) and use drag&drop to assign that pin as minus terminal for your port.