Sorry for the late reply. I cannot recall to have had this issue reported before. This version of DFFS is a bit dated (2014) so I would recommend that you update and check if the problems still exist.
If you have an existing licenses you are able to upgrade it (depending on the type) to a v4 license.
Unfortunately I don’t know what could cause this issue. Are there any custom code used to override the built in SharePoint delete functions? Are you able to delete if you disable DFFS? (uninstall DFFS and test – the config is not removed and will pop back in when reinstalling DFFS).