When adding a new plugin, be sure to set permissions for all groups to read and write. Plugins use configs.xml to write and read. If permissions aren't set correctly, plugins will not be able to write hence "forgetting" settings.
To set permissions, right click on plugins and select Properties then click on Permissions and select all groups/others to have "write and delete files". Click on Apply Permissions to Enclosed Files button and click OK.
Affected plugins: exportCSVviaFTP, ExportDataToMainServer