Is there a chance you could send me a link to your website for me to check what the problem is? It saves a lot of guesswork on my part and alot of time too, as I don't know which way you have added the logo, and you don't remember...so, we could go through a list of possible causes, and waste hours, days in the process. I spent a good while diagnosing someones website last night, only to discover the owner of the site had decided that because he did not want all the themes he deleted them, including base theme, which is a parent theme to all themes, and carries with it all the CSS rules for styling Moodle, and he wondered why the theme he had downloaded, one which I had built, did not work as it was on my website!
So Suzie, for all I know you may have uploaded your Logo to the wrong theme? LOL