I'm not sue it will help, but can you show us some screen shots of Word and ID with non-printing characters showing? Have you checked to be sure all tracked changes are either accepted or rejected and then done a Save As on the Word doc to force it to re-write?
Can you confirm the spaces are present to begin with in that Word document? There was a buggy Word version a couple of years ago that deleted random spaces when it opened older documents of its own (Word) file format. Microsoft acknowledges as much here: Word 2010 randomly deleting spaces between words - Microsoft Community
I am a Microsoft employee, I lead the Program Management team for Office Sustaining Engineering.
This is a known issue with Word 2007.
(If this is the case: Unfortunately I am not aware of any solution. Word deletes those spaces, and once deleted, there is no way of restoring them.)
I've already encountered this problem a long time ago and I fixed it saving the Word files into .rtf.
But I don't tell you it works now!