Those printer settings like for trays and duplex etc. are not related to InDesign but to the printer driver, or in other words they are OS settings (Mac or Windows settings). If you save the from the Printer setup for your OS (yes, I understand you can acces these system printer settings from within the InDesign printer dialog) and they do not stick it is an OS problem. So save Printer settings first at OS level, then save secondly the settings in InDesign as InDesign preset.
That doesn't even make sense. It worked every single time from within the print presets up until CC2015 so how can it be a OS setting? I haven't updated the Mac OS in over a year so I don't even know why or how the Mac OS would even play into it.
Settings specific for a certain printer, such as duplex options or tray selection, are printer driver settings and have never been part of InDesign print settings. You can reach the printer driver (that are installed in your OS) settings from within InDesign (and in doing so you are going to the OS driver settings) but they have never been part of InDesign print settings. You can select a saved OS saved printer setting as part of your InDesign print setting if that is what you mean.
If you don't believe me I am sure others can back me up here ;-) So even if it does not make sense to you, it is the way it is...