I am still experiencing the same problem. I am using store exporter deluxe for woocommerce version 1.6.5. There is no possibility to update to 1.6.6 for me..
I have the settings on UTF-8. It is becomming prety unconvenient because I need the export file of the transactions before I can order new stock. I can think of other ways to do it but it would be more convenient if it would work like it did before.