References are out of sync

I am working with sub-documents in a Word 2003 master doc.  Somehow, all my refs in my documents are now two places earlier in the text than they should be (either when edit the sub-docs or when I expand all the sub-docs and work with them unified).  Does anyone have any suggests as to how I can correct this?  It is a MAJOR problem for me (looming thesis deadline!).  Very many thanks Thom