From my experience the autosize doesn't always work, especially if your logo is large (see
www.bajafishhunter.com
for an example). So when the sizing doesn't work, you will need to edit the CSS for the logo to make it come out correctly. Which isn't hard if you have firebug. You can play around and get the exact changes before you make them.
I've never had a problem with auto-size do you have a thread on this issue so I could take a look.