alchymyth on "Issue with footer nested inside main box"

find the closing tag of the main div

however, with several validation errors in your site involving unclosed divs, identifying the closing div for #main might indeed be difficult.

start by fixing the errors, possibly starting all-over with a fresh copy of the theme.

http://validator.w3.org/check?uri=http%3A%2F%2Fshippingandfreightresource.com%2F&charset=%28detect+automatically%29&doctype=Inline&group=0

http://codex.wordpress.org/Validating_a_Website