Reading the Desktop Collage comments posts I set out on a little quest helping out unlucky users now that Stardock said they didnt want to update this Dream.
Ive have created a little tool that will help you manage different picture folder to better accomodate the lack of Randomness and Recurcive folder scan of the Desktop Collage Dream.
Here is a screenshot of the app

The tool works by recursively looking through the folders added and copying all the images it meets to destination folder. When copying image it renames it to something like: 0A59FDAC-96A6-4D5C-97BE-1AAD0CCD647E.jpg
A nice random filename 
Be careful though as there is an option to delete files in destination folder prior to copying the files. If you have pricesless collectibles in your destination folder they will be deleted if you check Empty destination folder.
This tool doesnt solve all your problems but it helps make Desktop Collage a better Dream.
Hope you like it 
http://www.hinc.dk/Rename/DesktopCollageManager.zip