This has been bugging me for a while. It only seems to happen with IE7. I mentioned it back in September:
http://modxcms.com/forums/index.php?topic=5403.345
When editing a document and clicking save I get the ’Are you sure you want to navigate away....’ message. Even though I am not navigating away, I’m clicking Save.
Looking around the net there seems to be issues with the onbeforeunload event in IE7:
http://www.nathanblomquist.net/blog/2007/10/12/onbeforeunload-ie7-woes/
So I’ve modified 3 files and it might have fixed it.

I’m not sure if it causes any issues and my coding at this level may be a bit iffy. I think I am on the right lines but maybe someone could verify what I have done and maybe adapt it if needed. All this is using the latest versions: MODx 9.6.3 and TinyMCE 3.2.1.1
1) manager/actions/mutate_content.dynamic.php
line 510 add: documentEXIT=true;
before
<table cellpadding="0" cellspacing="0" class="actionButtons"><tr>
<td id="Button1"><a href="#" onclick="documentDirty=false; document.mutate.save.click();">
after
<table cellpadding="0" cellspacing="0" class="actionButtons"><tr>
<td id="Button1"><a href="#" onclick="documentDirty=false; documentEXIT=true; document.mutate.save.click();">
2) manager/includes/header.inc.php
line 55 add: var documentEXIT=false;
before
var documentDirty=false;
function checkDirt(evt) {
if(documentDirty==true) {
after
var documentDirty=false;
var documentEXIT=false;
function checkDirt(evt) {
if(documentDirty==true) {
3) assets/plugins/tinymce3211/tinymce.functions.php
Line 254 add: if (!documentEXIT)
before
function myCustomOnChangeHandler() {
documentDirty = true;
}
after
function myCustomOnChangeHandler() {
if (typeof documentEXIT=="undefined") documentDirty = true;
else if (!documentEXIT) documentDirty = true;
}