I was called in to help debug another AC client's analytics and noticed something odd:

In the footer, once you open the wysiwyg editor it automatically comments out the scripts from the html with an RAEditor prefix in the comments. It seems to be caused by the editor in AC; as a work around we created the analytics scripts as files on the server and use an external reference merge to call it in. Works fine now.

Not sure if anyone else if having this type of problem, and I'm hoping AC has some insight into this. Thanks!

Yep - we had the same prob and lodged a support request. Your work around is a good one. Our work-around is to not use the 'switch to HTML'/'switch to wysiwyg' button, at the top of the editor, for editing anything contains scripts. Instead, we use the icon the looks like '<>' and the 'pencil' in the bottom left corner of the editor to switch between HTML and WSIWYG which doesn't seem to cause the script-breaking issue.

 Here's our summary of the issue:

 Since the wysiwyg editor has been updated in admin, a bug has crept in where if you make a change to the code in the HMTL screen, it can break all scripts. 

http://www.telerik.com/community/forums/aspnet/editor/adding-custom-javascript.aspx 

The 3rd party control RadEditor is hacking up the javascript.  We are adding a new snapin (Code Snapin or Javascript Snapin or similar) where you can put in javascript and not worry about it which will help users keep it seperate from their HTML.  Another option is to put it in a .js file and do an include on the page.

We are not sure what else to do, if we turn on the scripting like that link above suggests it actually runs the script when in WYSIWYG mode which is just as annoying and causes other things to break randomly in the admin...it's a lose lose from what I gather.  Why telerik would 'run' the script is beyond me.  The verse is they 'comment' the code out when in wysiwyg mode...then when we get the HTML from the control...it's commented.

We are looking into autoswitching to html view before we grab the html so that it is always uncommented...until then it may be best to separate the javascript into its own html snapin so you can edit the area.