I copied code from our live site (running windows server 2003) to a new QA virtual machine (running windows 2008). When I view the page source info its exactly the same, but the appearance of the sites is very different. Is this caused by the difference in OS, or am I looking in the wrong place?
The appearance of the sites is determined by the browser you are using. If the application is generating the same code on each server, then the page should look identical if viewed in the same browser.
If you haven't copied a CSS file from the live site to the virtual machine, this could explain the problem. If the CSS file isn't found then the browser just renders the content using the default font of the browser.
What browser/version are you viewing the sites with?
Another thing that could affect the way the site looks is if the default font settings (style and size) are changed on the browser.
The breakdown is the following