It could have been the star drive section from and the saucer section from another. When they put the two together they had a few system issues. Which is why it's back in space dock shortly after TVH.
If it is the Ti-Ho
, its' issues would make sense as they would've had to put a new warp drive and nacelles into the ship.
I'll stick with the Yorktown theory. Who knows just what exactly "The Probe" did to all it's systems. Could have fried them all out , seeing how there was so much smoke in the Captains transmission to Starfleet Headquarters on Earth. Also it is very reasonable to suggest that the repairs were not fully finished by the time that Kirk and company arrived on board, although we are not sure what time has passed since they got back from the past.
Also because personally I think I like that idea is because TOS in the planning stages the Enterprise was first going to be the Yorktown....