For a field to appear on the issue navigator, it must be valid for all the issues that a filter *might* return.
For example, if you have a field called old-issue-no and it only belongs to the project "imported" then it will not appear in the navigator if your filter says "show me issues in project 'Imported' and project 'Fred'". Similarly for issue types - if your field is only on "bugs" and you filter for "bugs and features", then it won't appear until you narrow your search down to just bugs.
Check the field "context" in the Admin -> custom fields list.
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