Same document and 2 PDFs made (1 in MAC and one in WIN) and compared with changes

I have worked on a document and I have made 2 PDFs, one in MAC and the other in WIN, in both cases made with the same script. When comparing in Acrobat, the report indicates differences, but the document has not changed.
Why does Acrobat show me changes when the 2 PDFs have been made with the same document and configuration?