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
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> 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