@meljen
It is stranger than that in that I don't see what you are seeing on Chrome on linux. So, it is even more specific a problem than just being a Chrome thing. I would guess that it is something to do with how your browser defines the window, and that definition messing with the javascript that creates the popup. But that is just a guess. The thing is that many people think that these popups are not core functionality of IH so I would guess that there is going to be little enthusiasm for code wrestling a arcane browser problem for this particular feature. Just a guess again though...

@Golden Synergy
There is a 'clean' version of the configure file, called dist-configure.php in the downloaded version of Zen. It will show you which lines should have '/' at the end of them and which should not.