Performing this from a Fiery driven printer you would set the page range to duplex and tray association as pages 1&2 from the Mixed Media option.
It sounds as if Page 1 is set to pull from the bypass. Set it to page(s) 1,2.
Note that the paper weight may prohibit the duplex. 300 gsm will not duplex. You could specify the paper as 210 gsm if necessary.