Board Thread:Question and Answer/@comment-99.117.249.202-20140729232504/@comment-25067771-20140729235558

You can toggle the 'Don't show R cards when upgrading' button in the settings tab. It'll prevent you from upgrading important R cards. I too learned the hard way.

Are your cards actually in the presents box, but have been kicked below the 100 card viewing threshold?

Otherwise, I'm not sure. Something like this hasn't happened to me before.