I am having the same issue as well. Tried replacing the file like mentioned above and still getting a blank Excel file with headers only. Using PHP 7.0.9 & Content Builder version 0.9.91 (build 252).
Ironically, with the same setup on the same server but for a different form the export is working fine. Only difference is the form that is working is an old form like a year or 2 old where is the form where the export is not working was updated recently to add additional fields. After the update, the export to Excel stopped working.