I am having a nagging problem related to window and door cleanups in walls. Certain walls seem to lose the opening for a window or door. Sometimes, disconnecting a wall from another at a T or L insection clears the problem, but when they meet again, the all openings in that wall disappear. It looks fine in plan view, but 3d aspects of the wall are affected. This problem is also inconsistant. Quite frustrating. I've a attached a series of jpegs that illustrate a current issue.
you are having cleanup issues! I'd find some good tutorials on Wall cleanups (google it)
I think there is some good ones somewhere online.
google autocad architecture wall cleanups