Great you've fixed it.
Had the same problem and checked for Compatibillity Mode, which was turned off. So I turned it on (sellecting for all users). Which made the problem worse. Now the Window popup happened not only on a particular link, but as soon as I started chrome.
Turning Compatibillity Mode off again fixed everything.
I didn't check the registry, but it appears that even if Compatibillity Mode doesn't show up as ticked, it must still somehow be selected in the Registry. Turning it on and off seams a quick fix without the need to edit the reg.
Hope that this works for everyone else too:)