Ah, that would be it. Kanban boards work off fix version, and rely on "fix version is empty or unreleased". If you remove the fix version, they can't answer that question, so they have to assume the issue is not for the board.
You can get rid of most of that - have a look at the board configuration and you'll see the "filter to remove released issues" relies on fix version. You can change that so it looks at other criteria. But the "release" button on the done column is always going to simply set a fix version.
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