Both of my boxers are rescues and they have a few things I've found that their afraid of that I think they'll never get over.
Rufus hates feet on him or too close to him. He jumps straight up like he's been stung by a bee. either its a personal problem of his or someone used to kick him.
Roxy pet her with your feet all you want she's fine but rush her with your hands above her head, (like you're going to pet her) and she ducks. She used to be real bad and pee on the floor, or run and hide shaking under a chair but has really become much more confident in the almost 2 yrs I've had her. She was obviously very abused.
She's attacked the weedwacker, Rufus it's the lawnmower.
Roxy particularly dislikes the gardeners and barks every week at them through the window.
Although they seem to barely notice lightening and thunder, (not that they've ever had to be outside in it).