I'm not sure what is happening here. Logos uses the series name for the title here. Unless my copy was mislabeled by myself or otherwise, it is misleading.
The Text Comparison tool uses the Abbreviated Title of the resources for headings. In this case you have the KJV Apoc-only resource as the first Bible in your text comparison and there is no 1 John 5:5 since it is Apocrypha-only. The King James Version with Apocrypha series has two Bibles, the KJV 1900 (Gen-Rev) and KJV Apoc. Choose the KJV 1900 instead of the KJV Apoc and you should get your results.
I understand this. I guess what I am saying is that the tool refers to this text as the King James WITH Apocrypha, using the series name instead of the resource's title. When I changed the series title in the info panel all was made clear. I just found it misleading when I first saw the message in the pic.
In the Text Comparison tool, when you are picking which books to use, you can select either the series or the individual books in that series (by clicking the arrow to expand the series). If you pick the series, then the order of books in the series is going to be arbitrary. In this case, you've picked the series to be used first, and the very first book that is getting selected is the Apocrypha, which does not have the reference.
To fix this, you will want to remove the series and add the individual books within the series. Note that you can drag the items in your selected list in order to rearrange them.