I just removed AjaxControlToolkit v7 from my project, and therefore replaced the ToolkitScriptManager with the standard ScriptManager.
Now after postback on iframe in popup window all script functions (including jquery, $ etc) are undefined. Just about everything on the window object is undefined. The location is correct and all the script files are there in the head. I put a breakpoint in the script file and when it tries to call a function defined in that very same script file it is undefined.
Any ideas where to look?