Hi,
I've faced the same challenge. For now I have needed to use non-modal window
(normal pop-up window) to do the job.
Reason for the behavior is probably somewhere due to that opening a modal
client-side window also halts the execution of client-side code that opened
the window for as long as the modal window is closed(think of the modal
window as if it runs in the same context as the window that opened it).
Modal window's opener property is null for example, so as if it would be
treated as part of the opening (calling) code, even though opened page can
be physically different page. New window is opened because modal window
needs to be closed at client-side to let the calling code to run again (and
optionally do something with the return value from modal window)