Are there any errors displayed when these ghost maps are loaded?
Is the time signature on the scene file correct?
Have you modified model files, and maybe saved them with different hierarchies or limb orientations in the file?
Is there any identifiable pattern on the objects that don't get saved? How they were created, whether they are a child of another object, etc? Are they model files, brushes, entities, or everything?
Can you upload an example ghost map that has not been resaved since the problem started, without all the assets it uses, just the file itself?