I was able to export to GEDCOM 5.5 with FTM16 and then inport back in. As far as I can tell the errors are stripped out. Thank God! I lost the indent spacing for the starting paragraph of all my note sections. I tried importing with indent checked off and it did not correct it.
I think most of my errors in the file were connected with books, as that is what the error report showed. I tried deleting all the books that were saved, but that did not work. I think it may have something to do with windows 7 and the vista patch??