By saying the code, I assume you embedded the Javascript onto your HTML skin file. I don't know the reason that caused the code to be stripped out, but it shouldn't. Have you try linking it to an external file? Or you could try using conditional rule for the browsers to just acknowledge the file when it sees IE6 or below.

Cuong Dang
Co-founder: Enliven, dnnGallery
LinkedIn | Twitter
I'm the author of DNN and Web Standards Wrox Blox

I haven't tried using the png fix yet, but here's how you might want to try putting it to keep it from getting stripped out.

In your html you can put <!--[if IE 6] --> your png fix <--endif->

Another thing not many people know is that you can render certain png files with transparent background even in IE6 with NO PNG FIX needed. I discovered this by accident one day when I was looking at some templates on the below site to get ideas how to create pure css skins. Here's the example that is filled with layered png files and no PNG fix anywhere to be found.

http://www.csszengarden.com/?cssfile=/213/213.css&page=0

It took me a while to figure out how they did it, but the fix is very simple. The png has to be saved as 8-bit Indexed. That's it, that's the whole trick!

Good Luck,

~Bee