I have a similar problem. Compared to WordPress 2.7.1 you have added a new function in WordPress 2.8 for the Dashboard panel: Appearance-> Editor.
In WP 2.7.1 the code in the editor was just a plain text file. In 2.8, a JavaScript (I believe) for syntax higlighting has been added. When I go to that page and click to edit on the rather large Header.PHP file for my theme Atahualpa, the browser freezes for more than a minute before the JavaScript is done loading and sometimes the browser crashes completely. That problem I can live with but the total disaster is that the script also randomly refuses to accept my edits.
This is a strong indication that the syntax macro is badly coded and inefficient.
I STRONGLY RECOMMEND THAT WORDPRESS MAKES THIS MACRO AN OPTION IN WP 2.8.1 AND HAVE IT DEACTIVATED AS DEFAULT, ALLOWING THE USERS TO TURN IT ON INSTEAD.
(In that way, the acute problem is solved, and the macro can be improved without time pressure.)