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
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