By CSS, do you mean actual CSS or the externally linked version? If it is actual CSS, you should have it externally linked anyway. No clue on the changing of Doctypes, but there might be a setting set that makes it expect the strict one.
Here's the markup for an external source of CSS
<link rel="stylesheet" type="text/css" href="styles.css" />
Now use make a .css file named styles in the same folder as your code is in with only CSS in it.
I would also look into using a better editor like Komodo, or the PHP version of Eclipse. Both are free.