I did not really understand if you were referring to single Docs being blank, or Docs category (taxonomy) pages. You mention categories, but that filter is for single docs, so you must be referring to single Docs. In either case, I could not reproduce this.
Other Notes:
The $docscontent line that you commented out is part of the content_filter for single docs. This content filter has been removed in version 2.0 in favor of a new template system.
In the new template for single docs, that line is now:
echo $Isa_Organized_Docs->organized_docs_content_nav();
If you want to remove it, it can be found about line 23 in /includes/templates/single.php.
New Template Files Make it Easier to customize the Docs
If you want your custom changes to remain intact through plugin updates, then first add a folder named organized-docs to your theme. In that folder, you can add these custom files:
single.php – will display single docs.
archive.php – will display the main Docs page.
taxonomy.php – will display the docs archives and docs category pages.
sidebar.php – will display the sidebar for single docs.
First copy the original files from includes/templates, then make your modifications. (You don’t have to copy all 4 files. Only copy the ones that you want to modify.) I hope this helps.
