Over the past few days, I've had it happen twice where the TIMEDOUT instruction doesn't activate the output as expected. The only way (that I've found) to correct the problem is to copy / paste the rung to a new Rung #, remove the old rung, and accept / write changes. I've never seen this happen with any other instruction.
In the attached screen-shot, turning on C97 would not cause Y0 to be activated at all. Copy / paste to a new location, and it works perfectly.