To reproduce: 1) create a full export of your site 2) un tar/zip the export 3) edit one file (admin_bar.settings.json) and change one value ("position_fixed": 1,) 4) tar up your entire config directory again 5) import the new tar.gz, with changes 6) notice the (incorrect) warning on the page: The uploaded configuration matches the current site configuration exactly. No changes were made.

This may be related to #640

GitHub Link: 
https://github.com/backdrop/backdrop-issues/issues/661
GitHub Issue #: 
661