I recently had a similar issue. I found that if I did not put all status into a column (even if no bugs matching the Scrum Board's filter had those statuses), then only a subset of the Statuses that were not mapped would show up.
For example, I added "On Hold" and "Needs Triage" statuses. Then I made a board with a filter that only included issues with those statuses. If only those statuses were mapped to a column, then when I looked in the "Plan" view, *either* the "On Hold" or "Needs Triage" issues would appear, but not both (the status that showed up depended on which column was ordered first). However, if I then took all the unmapped status and threw them in a placeholder column titled "WTF Atlassian", then suddenly both "On Hold" and "Needs Triage" issues would appear in the plan view.
No idea what the issue is here, it's a black box. I even diffed the bugs that showed up vs the ones that wouldn't (after exporting them using the Export to XML option on the bug), and the only differences were the bug titles, creation dates, and status ids).
For now, however, the "WTF Atlassian" column trick works around the issue.
(This was on Jira 6.0.6 BTW)
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