Re: CSS mystery…
Crank open inspect element in your browser.. I take it you are using firefox, safari or chrome.. And take a look at the chain of CSS files that are leading to the definition for container etc in your site.
That will tell you which files are being used, and which are taking preference? Are you seeing the chain you expect? Is your custom.CSS in there?
Are you sure bloginfo is returning the path you expect – did you check this in your web inspector?