In ns_shiva I have two command consoles. One in the marine start and one as an auxilliary elsewhere in the map. I'm running into a problem where the marines' starting resource node is a node near the auxilliary rather than in the spawn.

Does anyone know how the starting resource node is chosen, and how I might fix this?

Dunno if this works, but try opening the .map file in Notepad, find the team_command which is near Auxilliary, and then see if you can find the other team_command (the MS one). If the Auxilliary one is above the MS team_command, try moving it down below it (just copy the whole part and then paste it after the other one). I hope that made sense.

The game picks a team_command and builds the nearest node. In what order? I don't know.

Have you tried making that auxilary console start unbuilt, and then use a trigger_random to start at round beginning to trigger the team_command after some seconds later? Could you even target something like that?

you could also try and block the rt-node close to the auxillary cc with e.g. a small door, which you open/move away a few seconds after round start.
As for the un-/build flag, I don't think it would work, since it will only look for the position of the cc, not taking care of, if it's build, or not.

so for anyone who is interested, it appears that the resource node that is selected is the one that is closest to the command console that comes second in the entity list.