I don't know why I didn't try this before, I now feel incredibly retarded.
Looking at my events for the thingy, I decided to just remove EVERYTHING that wasn't literally transporting the player over to the next layout.
So I delete my actions that made a smooth transition, all the fade-in effects and global variables and **** and I try it.
GenkiGenga, you were right, I am going to kick my self. Can't believe I didn't bother to simplify the events before, jesus christ.
GenkiGenga, I formally thank you so much you have absolutely no idea how much I am happy to have gotten rid of that bug.
Me posting this and more importantly, you replying is what caused me to be able to fix this soul-crushing yet so utterly simple of a bug.
It might not mean much, but you are getting a special thanks in my game's credits. I love you. You had no idea how much this one little thing was tormenting me, I actually took a break/quit for about 3 weeks.
I'm so ****ing glad that bug is over...............