This has been happening for a few versions. The reason for this is that everytime you load a new file, the click handlers of all the buttons are registered again (and again, and again). I modified the plugin myself as follows to resolve this:
At the bottom of plugin-dir/views/plugin-editor.php and plugin-dir/views/theme-editor.php there are a bunch of lines that look like:
$jq('#plugin_fullscreen').live("click", function() {
Where ‘plugin_fullscreen’ is different in each line. I changed each of the lines to:
$jq('#plugin_fullscreen').die("click.wp-editor").live("click.wp-editor", function() {
Adding the .wp-editor namespace to the click event makes it very easy to remove (with ‘die’) before it is registered a second time.
– Monk
