I'm not sure about an external program, but as a workaround you could either a) just don't set it to shuffle, and it'll go through every picture in order until it uses them all, or b) shuffle the files yourself; i.e. randomly give each picture a unique number from 1-100, although that'll probably take a long time.
Also, check to make sure you don't have duplicates of the files, because that might be the cause of some showing up more often than others. Sorry, I don't know of any actual program to shuffle them for you.