Jon, A couple more thoughts:
Santa Fe 8913 is the Road name and number. The Model number would be on the Box. I'm not able to tell exactly what type of Loco this is from the Road number.
Does the locomotive have rubber traction tires? If so, please post a focused close-up picture of the bottom of the Loco so that the traction tires configuration is visible.
If you have already checked and verified the other suggestions from above, then here is more to consider.
Some traction tire configurations cause this type of issue and could be what's causing your loco to stall on one of the isolated track sections and not the other (if one has the the isolated rail on the inside and the other isolated rail section is on the outside). You could try reversing the direction of the Loco and see if it now works on the problematic isolated track section and possibly not the other.
If this is what happens, a relatively simple fix would be to take out and rotate 180 degrees the physical orientation of one of the isolated sections so that both isolated track sections have the same (inside or outside) outside rails connected to the ZW Common terminal. The existing connections to the Crossing Gate the would stay the same.
This solution would require the Loco to always run in the same direction.