Line Ending Not Preserved (CRLF)

I recently upgraded to version 6.6 beta. Since then the line ending is changing from CRLF on my end to LF on the other end. I made no setting changes when upgrading. The transfer mode is still set to binary. I did notice that the server environment end-of-line characters setting was LF so I changed it to CRLF. (I don't know to what this parameter was set before the upgrade.) This did not have any effect.