I figured it out (after spending over an hour). It was XAS.
Find in your scripts 'XAS - Initialize' for the method
transfer_player, which should be around line 700. You will find this line:
Go ahead and comment that line or delete it. I really don't know why that was even there to begin with, perhaps to reset some variables XAS uses, but that's a really lame way to do it. I'm not sure if this will bug out XAS, so be sure to test that script a bit.
For scripters: "Why was that the problem?"
In CCTS, Game_Map uses variables @climate and @old_climate. It relies on these variables to make the appropriate changes when changing maps (and climates). It assumes Game_Map is one instance that is never changed or replaced. However, with XAS calling a new Game_Map every time the player changes maps, @climate and @old_climate are deleted and initialized with the values of 0.
Also, thanks to this, I found a bug in CCTS...that I will now fix...