My very old camera would slow down if there were too many files in the folder on the card. Put them in smaller folders (camera called them albums) and it would be faster. If the principle still holds it might explain the folders thing.
I just stick the card in the reader, go into dcim, select all the folders, cut them and then paste them to the hard drive in a new sub folder.
Once they are on the hdd it only takes seconds to move all the images into one folder and delete the number folders that are then empty. Can't see you need a utility for that.