When you choose a directory as source and the names of the files are for instance: video1.avi, video2.avi and video3.avi and the output files are avi too, the name of the three output files are the same: video4.avi. So, at the end of the process you only have one output file instead of three.
When you choose a directory as source and the names of the files are for instance: video1.avi, video2.avi and video3.avi and the output files are avi too, the name of the three output files are the same: video4.avi. So, at the end of the process you only have one output file instead of three.