FrontPage lets you optimize HTML when you're designing your site (meaning in your development environment) or when you publish your site to a live Web server. If you take the latter path, FrontPage cleans up only the HTML that resides on the server. Your development site stays as is.
There's no reason to optimize HTML at design time. If you do so, you could permanently disable even very basic features you've added and wreak havoc throughout your site. The only time you should even contemplate using the Optimize HTML feature is when you're ready to publish your site. Publishing Your site covers the ins and outs of optimizing.