The reason the page is jumping to the top is not because something is being made visible, that should never cause a page to change its scroll position. The reason is the link itself for 'Close' on the video pop-up:
http://worshipfilms.mine.nu:8008/collections.php?coll_id=18#
When the last thing on the address is '#' it means to jump to the top of the page. I have a feeling (though I couldn't easily locate it in the code) that what that link's href actually is in the code is:
href="#"
If I am right about that, simply change it to:
href="javascript:void(0);"
and it should be fine. You may also want to get rid of some of that added code you mention in your post as it wasn't helping and didn't address the real problem.
One other thing, if the link is something like so:
Code:
<a href="#" onclick="closeVid();">Close</a>
You can also fix it by adding:
Code:
<a href="#" onclick="closeVid();return false;">Close</a>
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