Is the issue that the csv being downloaded has data that doesn't match or that it isn't formatted the same? The values coming down in CSV will be numeric and not contain separators such as commas as that would make the fields strings. If the data is changing on you then that's a different issue and we would want to see an example. That would probably require either sharing a workbook here or contacting Tableau Support to work through in detail.
I hope that helps.