As usual, Marty is on top of it. 
If for some reason the sensors are aligned, which is the top suspect for this issue, here's the next thing to check.
Check the wires under the heatshrink going to the sensors, I've had a few of them that broke off the IR LED in the locomotive or the IR sensor in the tender. You can see if one has broken loose by just tugging gently on them, usually one that's become unsoldered will pull out. Obviously, that's a problem.
