m dulin,
If you want your PDF settings in InDesign and Frame to match, you can open Distiller, set your options, and specify a watch folder. A watch folder is an empty folder you have somewhere on your computer. You may have to create an empty In folder inside the watch folder. Then to make a PDF from whichever application, print to the Adobe PDF printer and select Save as File, choosing the In folder inside the watch folder as the place to store the ps file. Once the application is finished writing the Postscript file, Distiller takes over and creates the PDF and puts it and optionally the ps file into an Out folder inside the watch folder. If you create a ps from the other application before Distiller is finished with the first, Distiller will handle the second file when finished with the first.
With this workflow, there is no need to set the PDF options each time within each application. You set them once in Distiller and leave Distiller running all the time. Furthermore, Distiller is handling the PDF creation part and the apps are just creating Postscript files; they do not Distiller from Adam. Moreover, you need not create your Postscript files with Adobe PDF, you could also use any Postscript printer connected to your computer because you are saving the Postscript to file, not sending it to the printer.
If this also causes problems, then as suggested by others, you may be having a problem with Distiller.
Van