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To prevent appearance of double scrollbars editor supports floating toolbar. When floating toolbar is enabled editor works in autogrowing mode. There are some config params to manage these modes.
To disable floating toolbar edit your LocalSettings.php and insert the following line:
$wgFCKFloatingToolbar = false;
Autogrowing in source mode is avaliable since Lyons. And now you can enable/disable autogrowing for WYSIWYG/Source modes separately. The following editor's config options are available:
FCKConfig.AutoGrow = true ;
FCKConfig.SourceAutoGrow = true ;
FCKConfig.IESourceAutoGrow = false ;
Unfortunally, this feature is disabled in IE by default because of IE's bug. If you'll set FCKConfig.IESourceAutoGrow to true you'll be unable to use native browser's undo/redo operations in source mode.