I also use LTN Tracker and Todo List which also add GUI elements to the (top) left of the screen.
If I have LTN Tracker and Todo List open at the same time, then the GUIs are shown side-by-side and everything works fine. If I open either of those GUIs and TheFatController at the same time, then the two windows merge and TFC's GUI takes on the width of the other mod's window, seemingly becoming the lower half of that window.
I also use LTN Tracker and Todo List which also add GUI elements to the (top) left of the screen.
If I have LTN Tracker and Todo List open at the same time, then the GUIs are shown side-by-side and everything works fine. If I open either of those GUIs and TheFatController at the same time, then the two windows merge and TFC's GUI takes on the width of the other mod's window, seemingly becoming the lower half of that window.