I'm not sure what the nomargin.js script does, I know nothing about java, so looking at it is about as productive as me looking at, well java!
You added the margin code to the #container, maybe try adding it to the footer and then the body if that doesn't work. If that's a no go, sometimes padding (for me anyway) does the trick, so you could try just adding
padding-bottom:20px; if there is none already in the div or just amend the padding that's there (top-right-bottom-left).
If all none of that works, then I am just as mystified as you - it's late here though, so I will blame any obvious oversight on being tired!
The sight looks great though! Even without the bottom space in IE, it still looks good! I'll check back on this thread tomorrow and try it again if the solution is still elusive.