I've just encountered an issue that is currently documented in this knowledge base article: http://support.microsoft.com/kb/936993

The article states that "This behavior is by design". This is unacceptable for a number of reasons:

1. The article actually provides the fix. What would be the harm in incorporating it into the released compiled library so that those of us affected by this problem can continue using the scripts from the resource files instead of having to maintain our own set of extraneous javascript files, not to mention having to copy them into every web site application that needs them?
2. We can no longer use the compiled version of AjaxControlToolkit. Again, we'll need to copy the js files out of the source code into a script directory
3. Any ScriptReferences for custom client objects that were previously compiled into external assemblies now require setting the ScriptReference.IgnoreScriptPath property, which isn't even included in a constructor overload for ScriptReference, which means extra work and extra lines of code.
4. FireFox does not have this issue.
   

I'm guessing that a growing number of people will be encountering this as a result of the release of Facebook's API. One of the most compelling reasons for developing an IFRAME Facebook Application instead of an FBML Facebook Application is the ability to use the existing AJAX Framework, but that will prove very difficult with this limitation.

So, PLEASE include the fix from the Knowledge Base article in the next AJAX release!
 

Damn, when will MS learn of Open Source ppl, i only have this problem on internet explorer, on the others browsers works perfectly.

Still, this didn't do any trick with me, cuz i couldn't fin the AjaxControlToolkit/1.0.10618.0 folder where some of the ajax source codes are stored, when trying to stablish the scripts paths in the scripts manager, i checked that it was calling the ones on the folder scripts like the documentation was asking, but it also was asking for the ajax control toolkit source files, and thus no finding em, it wouldn't load a thing

 
Seems like i'll have to do something, so when a user enters with IE won't load the ajax components and just show the info i have on the tabs, else, how the tabs.

Edit1:
Ok, i got the script from the ajaxtoolkit source (i only downloaded the one without the source files) and put em on the directory that the script manager is asking for, but still my ajax app won't show on the web page, any suggetsion why is this?
 

This is ridiculous.  I'm setting up a legitimate application and it cannot work due to the fact that it's running through another domain that is hosting it?  Microsoft needs to fix this BUG asap! And it definitely is a BUG