I'm using Drupal 6.12, FCKeditor module 6.x-1.3, and FCKEditor 6.2.4. Basically the latest versions of everything. Your mileage may vary.
I've been modifying the look and feel of Drupal's basic edit node page. Because of that, it was easy to modify the Drupal template so that the editor is 60 rows and 80 columns, but you don't need to do that. If you did anyway, you'd find like other users that when the editor loads, the window resizes to 420px. That's how I got here, and it was decidedly not groovy.
As others have commented here, the height resize is hard-coded FCKeditor behavior. Pretty lame, given there's an easy way in the admin section to specify the width but not the height. Here's how to change it:
Go to where you installed FCKeditor (e.g., modules/fckeditor) and open up fckeditor.module in your favourite text editor. (It's just a PHP file.) Change the following line (for me it was line #983)
". $js_id .".Height = \"". $height ."\";