Ok, that's good, and the screenshots are very clear too.
You definitely need to check the field configuration to see if the system priority field is valid for the filter you are running. There's actually a really quick and dirty test here - find an issue that has a priority set (check the issue view) and then run a filter for "Key = ABC-123" (assuming the issue is ABC-123). That should definitely show the priority in the navigator. It would be a useful test for us to chase down any other oddness going on too!
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