I did however notice something was a little off. And really I've noticed this before. When I switched from fullscreen, my system menu for the application would disappear.
So, I did what anyone who's not very bright would do: I stepped into it with the debugger, I tried a bunch of things in the immediate mode to restore the system menu, but nothing worked. Until I hid and re-displayed the window. Then everything was fine. So I implemented this in the mode reset code, it will now hide it before making modifications to the window (changing border size, topmost, etc...), and then redisplay it when it's done. Works fine.
So yeah, if you ever find your window is behaving strangely after a switch from fullscreen to windowed mode, hide it and show it.
You'd think I'd know this shit by now.