Woah... This shouldn't be happening..

[JenniferOrange]

(Just a quick suggestion..)
For your disappearing floors, have you made sure the Collide box is checked for the floor?
And if it's just not working then is your map rather large? I'm talking humongous. If it is maybe it can't take any more floors.
Also if primitive floors don't work, try static object floors, since they might not disappear. You can find some under either sanctum or cistern.. I believe it's sanctum, but I'm not sure off the top of my head. You can try placing the static object floor and see what happens.
Lastly my floors used to disappear when I had a .cache file. Make sure you don't have one, if you do, delete it!