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.
This is a strong indication that the macro responsible for line numbers, color etc, in the editor is badly coded and inefficient. As it can’t be turned off there is no way to handle this problem.
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 (e.g.:“guided editing”).
(In that way, the acute problem is solved, and the macro can be improved without time pressure.)