Did you delete the old image before changing the settings? Due to the way WordPress core handles images it is necessary to upload the image after the settings have been changed.
Let me go into a bit more technical detail: Internally image sizes are associated to a unique handle. In case of the logo this handle is 'enlightenment-site-logo'. In contrast the images that reside physically in the upload folder are associated directly with their size. This measure is to prevent orphaning of image thumbnails, for example when a plugin that registered an image size through a handle is deactivated, that size is still available to WordPress core. For that reason when an image is requested through a handle, an exact size match is performed and if not found the closest size is sent. That’s why when uploading an image before changing its settings sometimes results in a differently sized image. Since WordPress doesn’t resize images on the fly, those settings are necessary. So it’s important to always set the image size before uploading the image to make sure you get the right dimensions.