Make sure you have Send Image Data set to All.
And check to be sure the printer driver isn't set to Draft mode.
The Send Image Data is set to All, and the printer driver is not set at Draft. The same printer driver settings are used for both the InDesign and Acrobat printing so the problem resides within InDesign in some way.
Hard to imagine there's anything wrong in the file if it produces a good PDF, but check the links are up to date, too. And check the transparency flattener settings.
Long shot, but maybe reset the prefs (see Replace Your Preferences).