As Javascript is such a dynamic language it may be possible to patch this in your app rather than having to change the version of dojo that comes with Domino.

 

The following is an example of how you could patch the functionality of dijit._frames.pop() (the function that contains the problem you're seeing). This is similar to the way function decorators work in Python, though without the convenient syntax.

 

(function(){// This will prevent local variables such as dojoPopFunc from

             // polluting the global namespace

 

    var dojoPopFunc = dijit._frames.pop;// Save the dojo version of pop in 

                                         // the enclosed scope

 

    dijit._frames.pop = function(){

       // dojo._frames.pop doesn't take any arguments but using apply() like

       // this is a useful pattern if you needed to override other core

       // functions

        var iframe = dojoPopFunc.apply(this, arguments);

 

       // My guess is the IE9 is handling z-index differently than earlier

       // versions of Internet Explorer, you may need to try some other style

       // fixes to resolve your issue.

        dojo.query(iframe).style('z-index', '10');

    }

})();