EPMLCM-14000:Error reported from FDM Enterprise Edition. EPMFDM-140291:Export of scripts has failed since system directory could not be found
The code where the failure occurred, will execute only when exporting a custom, event, drill script.
Check if the Application Root Folder is also set in the Application Settings page, for all the applications that are being exported. (Setup Tab > Application Settings > Select the target application in the drop down > Check Application Root Folder entry).
If its a full LCM export, all the Applications in the drop down need to have the App root folder set. It can be set with the same value as in System Settings page.