Hi Rob,
This failing delete of folders after encryption is a known issue and has been fixed in the current beta of Boxcryptor for Windows v2.1 which you can download here:
https://www.boxcryptor.com/l/download-windows-beta
Sometimes third-party applications try to write to the Boxcryptor drive root and this can trigger this message. If you can reproduce it, a debug log could tell us which application is trying to write there and we can remove the message for this case. More information about debug logs:
https://support.boxcryptor.com/display/BCWINEN/How+to+create+a+Debug+log
Best regards,
Robert