Do you think that the "incodent" that happend with using the computers for something other than typing in the numbers was creating, or at least activating/fucking with the defense system, and thats why its going wild around the island now?
Also, i'm a bit suspicious about Walt being on the other end of the the computer. could it have been another who just used the word "dad" as in reference to realising that Michael is Walt's father? Walt could have used his name around the people that took him, and they made a connection when Micheal typed.
It is a bit ironic that as soon as they watch the video that suddenly there is talking on the computer though.