When a song plagues me like that it usually means there is something in the lyrics to fit a current situation, either "for real" or because whatever I internalized through the words is ready to be put under a microscope, but in either case, the song applies somehow to something I'm currently dealing with. Maybe it works that way with you, too.
Hokey or not, if you have all the words to the song I'd appreciate it if you'd post them. Sometimes it helps to go through line by line and see just where the logic goes bad, if it does. The only other part of that song I remember is "On many occassions God spoke long ago, by means of his prophets on earth here below". What else does it say?