Yes there is a difference, in the fact that the first one is wrong. But it is not a big mistake, so I wouldn't worry too much about it. It might just go as a typo.

You could write: "Qu'est-ce que ce logiciel?" or "Qu'est ce logiciel?" Both mean the same thing. The second sentence doesn't take a hyphen, the first one does, as you are using the expression "qu'est-ce que", as opposed to "qu'est". In fact, what you did with your first sentence was take the expression "qu'est" and follow it with the words "ce que ce", which makes no sense per se. But as I said, it is a minor mistake (unless you are a perfectionist, of course...)