Hi Mike, Don't change the switches yet. Yes the yellow controller wire is for the controller lamp. The switch will still light its lamp & nonderail works with controllers unhooked. Overall these are trouble free. It's unlikly all 3 switches are faulty.
You say trains run fine on both inner & outer loops. That means you have power & ground to the rails, but you can still have some odd issues.
Do an experiment for me. Take a jumper wire & hook it to the outside rails of both loops, which makes 100% sure the grounds are common. The switch is internally grounded so there is no need for a ground wire AUX GND. Take the track jumpers off & install your fixed volts wire to AUX IN. This means terminals AUX GND & TRACK JUMPER will be left vacant. Double check your controller wires: Yellow to RCS LIGHTS, red to OUT, black to GND, green to THRU. Do this on all 3 switches.
Now, again run trains & make sure both loops can run trains properly.
Now, take your AUX IN wire(S) & hold it to center rail of the outside loop with the throttle on 50% or so. You should see the laterns light & the switches should work. If so you know you infact actually have a common ground & the switches work. You know for sure you have power at the outside loop center rail because you just ran a train on it.
Now, hook the AUX IN wires to the transformer. If no work you are not getting output from that transformer terminal.
I'm going to touch on voltmeters. They can trick you on simple circuits sometimes, because you can measure voltage, but you actually have no current flow. One tool that is very old school is a test lamp, as they require current flow to light the bulb. For track & switch power issues they are hard to beat. With just a little practice you can get a good idea of track volts by the brightness of the bulb, just as you can from incandesant loco headlamps. Do not use test lamps for electronic circuit board diag as the bulb can draw too much current in this case. But in the diag you are doing they are hard to beat.
Try this test & get back to us.
Very best, Don Johnson