Presumably the generated output (as opposed to the published output) displays OK when you view in IE? If so, has your published output EVER worked using IE? If so, it time to do some detective work starting with your server administrators.
I'm a bit confused here. When you publish, you are simply copying files from one location to another. No browser is involved. When you generate, you are creating the files that the browser will present. But again, no browser is involved in the process.
Are you perhaps meaning to say "When I *VIEW* the generated files using IE 8 or 9"?
Yes, that is what I meant. Thanks.