it sounds like the IIS site isn't setup the same.
When you run VWD (F5 run) you get a root site. Something like
http://localhost:1234/default.aspx
So in that case, all your URL's can just be root, or not qualified.
Check the source of your page. You'll probably see something like
<script src="/whatever.
js"></script>
This is expected to be found in the root of your site. And if fact it is, and is found when using VWD.
Now, over to IIS.
You probably setup a Virtual Directory like /MySite/
So it runs under
http://localhost/mysite/default.aspx.
When the same source is served out, it errors because it can't be found.
<script src="/Whatever.
js"></script> is looking in
http://localhost/Whatever.js and it can't be found there.
Just a guess, but that's probably your problem.
either way, give us some more details, and we'll see if we can get it running for you.
-=- Scott Cate