It seems to be a bug in the latest version. We have created an internal bug to track this issue. Thanks for reporting the issue and sorry for the inconvenience.
To clarify on match source rewrap for DNx vs match source for H.264; when rewrap preset in DNx is selected, video frames from the source are copied to the output (called smart render) without decode and then re-encode of the video frames, so this option results in faster render times preserving the source. The match source preset for H.264 tries to match the output setting with that of the source setting, but it will result in re-encode (decode & encode) because we don't support smart render for H.264 output. This also means with match source for H.264 you can individually match source basic video settings while you can't do that with rewrap preset.