For those who are experiencing this issue years later; I eventually worked out a solution.
What I learned was that, when this was happening, if I exploded the lines, saved, closed and re-opened the file, I then often found extremely high or low Z-values on the vertices. Usually near or at the upper or lower limit of a float. For some reason, when this happened (it's an issue I no longer have since I upgraded), the elevation of the lwpolyline and the Z-value of the 3D polyline both show zero. Even if I just exploded, the lines would show a Z-value of zero at each vertex until I saved and re-opened.
I then found that using Lisp; I could access those z-values without having to save, close and re-open the file. So I wrote a script that flattens the drawing in a way that works. Please excuse my lack of explanation as to how it works, as I frankly don't remember exactly. If I recall correctly, it directly modifies all of the entities in the drawing that might be affected by this issue so as to ensure they are all set to zero Z-value (basically, it overwrites the vertex coordinates with X, Y, 0). I wrote it years ago (a couple months after my last post here). There are two functions in the file that use a "*.ini" file (just a text file, not a traditional INI file) in a hard-coded folder: you should change those to suit your system. Once this file is loaded, the command "DFLAT" should fix this error. This was written for ACAD Civil 3D 2013, I believe.
I'm a little surprised to see people still commenting on this thread years later, so hopefully this will help someone. I don't recall this function ever not working, so best of luck.
