Spoiler Alert:

The "isos" were the weakest part of the film for me. Well, one of the weakest parts. They're pretty much entirely the reason why I tell people that Tron: Legacy really isn't about computers at all. The isos were a plot device that made no sense. Programs that are somehow created spontaneously without interaction, foreknowledge, or action on the part of the programmer?

It's the exact same thing they did in I, Robot, with the "random bits of code." They wanted a magical explanation to spoon-feed to audiences that at once would hand-wave any non-technical questions ("Why would a robot have feelings?") and also sidestepping any technically pertinent questions ("What purpose would feelings serve in a robot?").

To me, it's like the writers were saying "We don't know either."