I believe Walt to be the one who is controlling the computer and trying to send them messages when he can through hologram images in the jungle. Hence the image that Shannon and Sayid saw, in reverse. For whatever reason, he figured out or got a chance to get to the other's computers when they weren't looking.

I Think this is how they're going to explain that anyway.


Just my opinion.

He does seem somewhat technically savvy, as most kids now are. Man...when that message came up, I almost screamed!