If that original part of the program that allowed for self-modification wasn't a catalyst in any way, then yes. Maybe the changes become so frequent and byzantine that an origin can't be readily be identified. But in effect, the computer would still be a wind-up toy. The problem with free will is that it can't be given. Does any computer do things because it wills, outside of reaction to circumstances already accounted for in the program? Behaviorists might argue that men are slaves to the codes in our brains or in our DNA just as computers are slaves to their programming, but it's not nearly a neat enough comparison. There are differences as well as similarities between brains and CPUs.
But I make no suppositions about a creator who winds us up. I'm not going there.
<{POST_SNAPBACK}>
You limit the notion of computers. There are also neural networks, which function exactly like network of neurons in human brain. The assumption that "computers is just a wound up toy" is not correct.