We have also tried to deactivate the plugins manually, one by one to see if anything is in conflict with Cornerstone or X Theme, however, we could not find any. The issue still persists on the live site after troubleshooting.
We tried to update the theme and Cornerstone plugin on the staging site - http://41k.9c9.myftpupload.com, however, the updates did not break the frontend of the site. Please see screenshot of how it looks after the update - http://prntscr.com/jzb6le. We are suspecting that since the theme is not validated on the staging site, the changes/issues do not reflect on the staging site.