Anytime I log-in to Expedia, my entire Groupy bunch is poked into the lower left corner of my screen and the windows are all but minimized.
It would not be Groupy that is being affected, it's the browser that you have grouped that is reacting to a pop-up.
One thing you may try is enabling conditional grouping - using the Shift key to group option for example:

That way, any popup is not auto grouped and should not be yanked anywhere.
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Sean Drohan
Stardock Customer Service Manager