In content/edit.php:

        $obj->cleanupInternalDrafts();
        $version = $obj->createNewVersionIn( $EditLanguage );
        $version->setAttribute( 'status', eZContentObjectVersion::STATUS_INTERNAL_DRAFT );
        $version->store();
        return $Module->redirectToView( "edit", array( $ObjectID, $version->attribute( "version" ), $EditLanguage ) );

"$version = $obj->createNewVersionIn( $EditLanguage );" starts and commits a database transaction, and the 2 lines after are not in a transaction anymore.

Suggested solution: add a new parameter to eZContentObject::createNewVersionIn(), which specifies the status for the new version (by default eZContentObjectVersion::STATUS_DRAFT). Here we pass eZContentObjectVersion::STATUS_INTERNAL_DRAFT. We will also spare a SQL query with doing it this way.