There are couple items that you should check.
Make sure your are editing the skin in \data\sites\[sitenumber]\skins\[skin-directory]
Turn off CSS caching while you are making skin changes. Add these lines to your user.config and then "touch" the web.config.
<add key="CacheCssOnServer" value="false" />
<add key="CacheCssInBrowser" value="false" />
Don't include quotes around the commented out section in the style.css file. (you probably didn't but I just wanted to make sure)
Make sure you are closing the SiteLogo control, what you put in your post isn't correct.
<portal:SiteLogo id="SiteLogo" runat="server" />
Placement of the control depends on the skin but to make it appear on the page in the correct place, you will need to modify the CSS that controls it. The CSS class that controls it is .sitelogo.