If you check "Mark all edits minor by default" all edits in Thread: namespace which add new replies or threads are marked as minor (and viceversa, I suppose) and you don't have a checkbox to change that.
Example: http://strategy.wikimedia.org/w/index.php?limit=50&title=Special%3AContributions&contribs=user&target=Nemo+bis&namespace=90
Bug 21700 says something different.
Version: unspecified
Severity: normal