It might be because you set both normal & retina logo with the same image. The retina logo size should 2x (twice larger) than the standard logo size. In this case, your standard logo size is: 342×85, so the retina size should be: 684×170. If you don’t have the retina logo, just leave the option blank so the normal size should not be resized.
For ads setup, you can find the option on the Appearance > Customize > JNews : Advertisement Option then navigate Article Ads (for the post) and Header Ads (for the header). For more complete information, you can visit our documentation about it here http://support.jegtheme.com/documentation/advertisement-option/.