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 ."\";
". $js_id .".Height = \"100%\";
That will make your editor resize to whatever container DIV constraints you have. You can also change $height to whatever you want. E.g., 600 pixels high would be
". $js_id .".Height = \"600\";
What's going on here is $height is a variable that is "guesstimated" based on the # of rows you have. Dealing with the logic of all that is pretty simple, but left as an exercise for the reader. Also, standard Drupal warnings apply: you might need to clear your caches and you'll lose your changes if/when you upgrade the module.
Now obviously, this solution pales to one having the window auto-expand or at least having a manually resizeable window (like the default Drupal textarea is). If someone has done this, please respond, otherwise y'all will have to wait until it bugs me enough to move to the top of the list of things to do. (Hint: it probably can be done by editing the same file!)
Many Bothans died to bring us this information.
Hope this helps!