After a long time of not knowing why the teleporting system was only working some of the time, GamerGull informed me why. The triggers were set to center activation rather than overlap activation. I am told that there might have been an issue moving between updates that has effected the 'center' option of the trigger activation types, but 'overlap' activates if something collides anywhere in the trigger zone, so it really doesn't make a difference for the purpose.
Thank you very much GamerGull.
I will be doing some more work on this mod soon.