Sometimes JIRA does not show custom fields added to the result list in the configure column dialog and only after adding those columns to the query, the result list will display them. This seems not to occur, when a simple query is executed, such as "Issuetype = Defect", then the desired columns are all displayed.
We are using JIRA 5
Ah, I was about to say much the same.
For a column to appear in the navigator, it must belong to every issue that the filter *might* return.
e.g. if you have a field called "fred" that only exists on "Bugs" (by virtue of the "context" settings for the field), then if you run a filter for "bugs and features", you won't get the column displayed. Because "features" don't have "fred".
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