Trials and tribulations of the Odyssey
Okay I've got it. The transwarp drive is still a bit of a mystery. They built it with scavanged parts and with tech and theories that only a few people can barely begin to comprehend. This highly experimental and theoretical piece of propulsion technology unfortunately has an effect on its own sub-space field leading to creations of time-space oddities everytime they use the transwarp drive for more than a micro-jump of 500 light years (or something, I'll work out the figures later) so when they leaped all the way from the Utopia Planitia Fleet Yards to DS12 they caused a minor disruption in the time space continuum and for a micro-second actually changed places with a more advanced version of the Odyssey from a parallel dimension where all Starfleet vessels have sentient computers based on 'ancient technology of a race that had destroyed itself by trying to meld themselves into machines' :).
However, when time rights itself the sentient computer has changed places with its more mundane counterpart. The crew don't notice the problem until the ship starts upgrading itself (in borg-like fashion - red herring city) and when the ship's computer actually back chats the CO.
That as they say is that. Comments.