Without looking at any of the code at all, there's a general way to stop the default action when you're using Javascript instead. For example:
<a href="..." onclick="dothis(); return false;">
Basically, instead of loading the link it will "dothis()" (some function, like maybe loading a popup window), then return false, notifying the browser that the action is complete.
A shorter way to write it is:
<a href="..." onclick="return dothis();">
So it just "returns" (read "does") the function, and then stops execution.
To apply this to your page, just find the part where the "scrolling" event is captured and add a "return" like above. Because this is actually several events, you may need to add it in several places.
Depending on how complex the code is this may be very difficult to do, or even impossible.
There are probably some other ways to avoid this issue entirely, such as setting some property to the div where scrolling is self contained, but I'm not sure how you would best approach that.
If you need more help, please post a link to the page on your site that contains the problematic script so we can check it out.
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