I've noticed that since the update, my docked power-reactors don't stay on. they have a logic clock that makes them provide power to the ship, which I can toggle on or off. If I turn them on, leave the game, and reload the game, they're off, even though I left them on. This didn't happen before this update (not sure about this hotfix though). Also, these docked power reactors do work with the old docking modules, but not with rail docking.
Also, when I save and load in the ship, the power reactors also are not activated, even though I saved it with the power on. In case it makes a difference, I'm playing single player.
Another bug I've noticed is that wireless logic modules on a docked part of a ship don't stay connected to another wireless logic module on the mother ship when I save and load a ship. I've seen on the community content page that somebody else was having the same problem with their ship.