If you visit the source page for Shadowbox on github you will see that it has been updated recently as of late May 2011, just a couple of months ago!
If your hosting JW Player file at your site you may wish to update that file from JW LongTail Video.
I am curious why you think your cyber-attacks of viruses are happening from your installed Shadowbox.
I think the root of your problem is beyond any lightbox integration.
When posting your markup here on the forum follow these simple steps:
0. Login and paste your markup into the Message Box.
1. Mouse select the markup you just pasted.
2. Press the More Button from the Message Box Toolbar.
3. Select Raw text from the drop down menu. DONE!
If I don't respond to your POST, it's your inability to provide your markup correctly.
Check out a few DEMOS I made that are here in this forum.
I hope you find what is causing you problems, but I am 100% confident that this assumption is false. happy coding