Entries object getting reset after a relatedTo query
Based on the bug report found here (https://github.com/craftcms/cms/issues/2160), I am now creating a variable that contains all of the items prior to filtering it.

{% set entries = craft.entries.type('publications').orderBy("postDate desc") %}
{% set allEntries = entries.all() %}


I can then use entries to filter through the available categories and then use allEntries to loop through all of them.

I understand I could also have used clone() to get a copy to work from in my category loop. 

{% set catEntries = clone(entries).relatedTo(cat) %}