We upgraded to 5.2.7 last week and discovered what appears to be a new bug. Columns containing Custom Field data do not display after being added via Configure Columns.
Steps to reproduce:
1) display a list of issues in Issue Navigator
2) use Configure Columns; add a column representing a custom field
3) return to the Issue Navigator and note that the column you added is not displayed.
I made other changes, such as moving and deleting standard columns, and that works fine. The problem appears to be related only to custom fields.
Have you checked this KB out https://confluence.atlassian.com/display/JIRAKB/Custom+Field+Not+Appearing+in+Issue+Navigator+Search+Criteria
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