Possibly Stupid Question (Doom Builder 2 issue)

So, I've been working on my map and everything has been fine and dandy, however later on I needed to make another sector in the very first room I made. The only problem is when I make a sector inside of it, it acts like I'm making a brand new one outside of the map. The walls are always impassible and in 3D view the sector floats in the middle of the room.

I've never had this problem before, does anyone know why it's doing this? I can make sectors just fine anywhere else in my map, but the very first room I made seems to be bugged...

EDIT: Okay, I booted up Doom Builder 2 again, and now it's not doing it. So I guess you can ignore this, but if someone wants to tell me what causes this still that would be cool.

This problem has been around in DB2 since ever and it regularly returns, and yet I've never seen anybody explaining it. I have experienced the problem myself, several times. It manifests itself when you're making a sector inside another sector, but only rarely and, what's important, only on certain exact places. Building the new sector on a different place within the bigger sector, and then moving its vertices to the intended places, seems to work to get around the problem.

Have you tried drawing the sector in the opposite direction?