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The code that Flash outputs is not standards compliant and embed tags do not validate because they are not part of the XHTML standard.

Note: The following series has been consolidated into one article here.

Dump the WYSIWYG
Do not use markup for presentation
Include a proper doctype
Validate your markup
Validate your CSS
Build for Firefox and hack for IE
If you have a problem ask for help

Let’s go through each of these steps in greater detail

Let’s face it. You can either be a part of the problem or a part of the solution. If you are allowing an application to turn out your markup then, unfortunately, you are a part of the problem. Yes, this includes Dreamweaver and GoLive. I am thoroughly convinced that these “web [...]

Tables are meant to be used for one thing and one thing only and that is the display of tabular data. Please, do not use tables for layout. It is much better left to CSS. Using tables for layout is a messy hack often used to “get pages to look the same [...]

You start your sentences with a capital letter; start your HTML with a DOCTYPE. It’s just basic grammar. - Mark Pilgrim from Dive Into Accessibility
Using a complete doctype will switch your browser into standards mode. This will cause it to render the page exactly as you have instructed it (which may look awful but [...]

Developing a website without validating is like running around with a blindfold on. As soon as you ask for directions, don’t be surprised if the only answer you’ll get is “take your blindfold off”. - some guy named Jim
Validate your markup here
Validate your CSS here

Firefox is a standards aware browser. The authors are actively involved in squashing bugs and making it work the way it should. When FF is switched to standards mode with a proper doctype everything works as expected.