This may be happen when you switch between using Virtuoso-XL and Virtuoso-L.
If you make edits in L, it is possible that objects related to connectivity are not properly cleaned up by the editor.
This was a problem in earlier software releases.
You may have some route objects or steiner points that are in the database and are resulting in a larger than normal cell boundary. These are not normally visible, but they have coordinate information that will mess up the display
Try using the following SKILL command (in XL) to clean up the connectivity:
Then re-run the extractor (if you want connectivity in your layouts).
This should remove the steiners and any other phantom route objects.
I hope this will fix your problem. If not, re-post. I may have another idea.