That link you provided didnt work. I set up a site with my template, but I cannot seem to reproduce your issues. Perhaps you can tell me what I didnt do?
http://d0wn.net/
Much of the JS is unedited from the modxhost template, so I dont see why that would effect it.
As for alpha PNG’s, there are numerous pages on how to get them to work, but the only one that really works is to set the style of the element to have a background of the image, then do the IE comment hack to add the big filter line. I have had no luck with the JS methods or the behavior.htc methods. Perhaps I’ll write a snippet to correctly display alpha pngs when I get the time.