I’ve noticed that Spaces and Ceilings can affect Revit MEP’s ability to display the Space element. I’ve seen it happen and then later correct itself magically. Not likely that it is magical, more like something was adjusted that changes the conditions in the first place. I admit I don’t know yet what that “magic” is.
The conditions for this to occur begin with the addition of a new Level to manage plenum areas in the building. When this new level is added and a view is created it’s a good idea to adjust the view range so it matches the available distance between boundaries. Initially it would be easy to expect this to be the reason that a Space doesn’t show up. When we add a space this error message will usually pop up.

Changing the elevation of the ceiling or the level or some combination will result in Revit being able to show them again. I created a
VIDEO that
DESCRIBES how the ceiling elevation and the space properties conflict with one another.
[Addendum: January 25,2011]
The issue described above has to do with the Room Computation Height of the Plenum Level, which is a Level Type parameter. The typical Level Types in Revit Templates set the Room Computation Height to be “Automatic”. This really means that the default is 4’ from the Level unless Revit encounters objects in/at the 4’ level. If Revit find issues, it adjusts the Room Computation Height to the Level plane instead.
In this case, the Level type (used for all the levels) uses the Automatic setting, so Revit defaults (when dealing with the Plenum Level) to the Ceiling Level to find the Space extents when it encounters the slab at the 4' elevation. When the bottom edge of the Ceiling Element gets nudged to align with the Ceiling Level, Revit can no longer find a closed circuit.
The solution here, and one that can be generally used, is to create a new Level Type to use for Plenum Levels, and explicitly set the Room Calculation Height to something like 0’ 6”, so the Space will always be cut inside of the Plenum Space.
Thanks to Kyle Bernhardt for the explanation!