I was running into the same problem. It turns out the printer driver didn't know that the "duplex unit" was installed (even though it's a duplex printer). Go to Control Panel -> Devices and Printers. Right click on your duplex printer and select the Printer Properties dialog (not to be confused with the inexplicably different Properties dialog), and go to the Device Settings tab. Tell the driver that the duplex unit is installed. The option for two-sided printing will then appear in the Acrobat print dialog. (This was a Windows solution, but it may be similar for Mac.)
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