Is my javascript overriding my other script?

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Javascript

CSS

HTML

HTML5

Okay, so I have some javascript code (seen here) that creates a Mac OS X-styled fisheye dock menu. I also have some code (seen here) that creates DHTML windows so that links opened on the webpage don't require the user to leave the page, they just open in mini div iframe windows within the current page. My problem is that when I open/close/minimize/resize any DHTML window, it suddenly disables the mouseover "fisheye" effect on the dock, just leaving the dock as a boring panel of link images. This happens on and off between Chrome and IE, and I cannot figure out is wrong with it. Could you please enlighten me? Any suggestions? I feel like the JS files responsible for the DHTML is cancelling out some function in the dock. Any help is appreciated. Thanks.