Thanks for the information and the screenshot. I was able to reproduce this if the modal browser popup was launched in the remote IE recording window.
Have you tried launching the popup in the Visual Studio recording window? When launching the popup there, a 'Connect to modal pop-up window...' test step should be recorded.
The WebUI popup tool bar will not be attached, but you should also be able to record clicks and typing in that popup window.
Please post back if it is not recording on the popup when launched from the VS recorder.
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