config.php

$baseUrl = '/images/'; 
$baseDir = resolveUrl($baseUrl);

and at the bottom of the configuration file, where resource types are defined use only one:

$config['ResourceType'][] = Array(
      'name' => 'Files',
      'url' => $baseUrl, // <-- Note: I have changed it
      'directory' => $baseDir, // <-- Note: I have changed it
      'maxSize' => 0,
      'allowedExtensions' => '7z,aiff,asf,avi,bmp,csv,doc,docx,fla,flv,gif,gz,gzip,jpeg,jpg,mid,mov,mp3,mp4,mpc,mpeg,mpg,ods,odt,pdf,png,ppt,pptx,pxd,qt,ram,rar,rm,rmi,rmvb,rtf,sdc,sitd,swf,sxc,sxw,tar,tgz,tif,tiff,txt,vsd,wav,wma,wmv,xls,xlsx,zip',
      'deniedExtensions' => '');

This way you'll have just one single folder in CKFinder, called "Files" that points to your images folder.