Further update on this problem:
I’ve discovered that the blended waypoints were not the root cause of multiple skipped waypoints. The skipped moves were inside of an if statement which was checking an input for high or low signal, and there is a problem with that input being interpreted as low even though it is high. Because this program started off working, began having this problem intermittently, and now has it all the time, I suspect hardware failure or damage of some sort. I will make a new topic describing that problem in more detail and link it to this one.