We are also having the same problem with this. We have tried using the Ajax Control Toolkit v3.0.30930 which is the last one which doesn't depend on the ToolScriptManager, but even with this we get the same error during postback when partial rendering is enabled on a module. The error only occurs when any AjaxControlToolkit controls are added to the page, e.g. ValidationCallout etc.
In an attempt to sort out the issue we tried to upgrade the Ajax Control Toolkit to the latest .NET 3.5 version (v3.5.51116). Even though several workarounds seem to have been documented on how to get this work, i.e. by adding script redirects etc. not seem to work. The DNN 5 option of adding the ToolScriptManager in Default.ascx can presumably not be applied here as replacing the RadAjaxPanel in DNN6 with the ToolScriptManager might cause other unforeseen problems. Even if these hacks did work, they are not a viable option for a re-distributable product as the end user cannot be expected to make these changes. My guess would be that if the Telerik RadAjaxPanel inherited from ToolScriptManager rather then ScriptManager then the latest AjaxControlToolkit should work OK. Obviously presumably it isn't as easy as that as otherwise this solution would already have been implemented.
In summary, DNN6 causes errors when AjaxControlToolkit controls exist in a module. I can't be certain whether this is because DNN6 isn't compatible with v3.0.30930 of the Toolkit as I can't get it to work at all with a later version to test.
Actually, it seems very surprising that there appear to be so many problems with DNN6 and the Ajax Control Toolkit. This is one of the most widely used control sets so I'd hope a resolution to this will be found fairly shortly as we cannot upgrade any of our sites to DNN6 until a solution exists for this.
Would someone from DotNetNuke or Telerik be able to comment.