Parent text frames

If on your parent/master page are primary text frames, you should click to place text without holding the shift key. 

I think you are confusing primary text frames with the auto-flow (shift-click). 

To "retrofit" primary text frames on a parent page (in case you didn't select the option when create the file), you need to link the left/right text frames. Not necessary if not using facing pages. Then you simple click with the Place icon on the first page (not shift-click). Be sure to check your preferences for adding and deleting pages when using the primary text frames. Primary text frames are locked by default like all parent page items, but by clicking on it with a "loaded" cursor, you will unlock them and flow your text into the pages. 

If you decide to shift-click to flow the text, you don't need primary text frames on the parent. This will automatically flow available text, creating its own frames. This feature will not automatically add more pages (or delete them based on preferences).

Basically, you pick one method or the other, not both.