It seems to be a problem with both Bizhubs (specifically the EFI Fiery Image-Controller drivers) and InDesign. My InDesign references the only PPDs installed for the Bizhubs, and all add-on options like duplexing have been set correctly in the drivers via Windows Control Panel, else they'd be grayed-out in the Fiery driver dialogs.

InDesign has always had a funny way of dealing with PostScript (PS) printer drivers (PPDs) that no other program does; so did PageMaker. I work in a print shop and print often to Bizhubs from other programs, namely CorelDRAW and MS Office products (Publisher, Word, etc.). Only InDesign won't properly save Bizhub PS Fiery settings from the print dialog. Maybe because Fiery is practically another program in itself.

But I think I found a slight workaround: When you print in InDesign, if you click Setup, select the Bizhub PCL Fiery driver, click Preferences, click OK, then select the Bizhub PS Fiery driver and click Preferences, make changes, and click OK, the PS print settings for that session should save. It did for me anyway.

The only real use for the Bizhub Fiery PCL driver is for "simple stuff" like Word documents. Most DTP programs print best to the PS driver.