It is actually missing the diesel and electric engines. When I open the repair list screen, they are just gone. I thought it was funny at first...
As to the ship pack mod, I don't remember which one it is. I have removed it from my active mod list.
Edit: Also, I was activating ISP after the ship pack mod to make sure that the updated physics applied to all the models. At least, that's what I thought I was supposed to do...