It is always recommended to export a PDF as single pages first. Print from Acrobat, make composing in the Fiery.
Printing from InDesign is not so good.
Printing from InDesign was always good!!!! Only in the new version CC 2017 it is crap. Please solve it.
Things such as Booklet Printing, Staples, Folding, 2 sided, setting the document to Hold instead of printing directly, etc etc.
So the problem is with the printer specific settings (Print>Printer...), and not the InDesign Print settings? If that's the case it seems like the fix would have to come from EFI.
This started happening right around the time I upgraded to Adobe CC 15.
Have you tried dropping back to CC2014 as a test? Your subscription lets you run multiple ID versions from the same computer.
This happens to me as well: was happening with at least 2015.4 and still happening with 2017. I'm on Windows 10. When printing from InDesign, it always uses my default printing preferences (which for me include double-sided and "offset jobs"). Whatever I select in the Fiery dialog is ignored. Works fine from all other software. Like you I just print everything from Acrobat now if I need different settings, or quickly cancel it via Command Workstation and put in new settings.
I have been running CC2017 since November, and just today I no longer can select my settings. However, this plague only effects two of my 6 trays. I can select all of my options and print normally straight from Ps, Ai, and Id from all of my small format trays. I called tech support and they said there is no solution.