No! Never had that problem. The thought that InDesign degrades the image in any way is a little ridiculous. Some thing else is going on. How are you laying it out in InDesign?

Use Bar code producer....It creates a wide range of Bar Codes including the QR...

In the Rampage Preferences: Uncheck "Enforce unique page name.......at the bottom of window.

Use a "CODE 128" Bar. You can use Alpha/Numeric as well as punctuation marks.