Sometimes it's emotional baggage and sometimes it's just the personality of the cat. Understandably many cats have been thru some horrific experiences and would remained scarred.
I've had my two boys since they were 8 weeks old with no sign of trauma. However, you'd think they were beaten every day of their lives!! The slightest noise makes them JUMP regardless of where they are. A few times we've been givin the luvs on my lap or in my arms and something has scarred them and I've been gouged so badly it scared me. Calvin once got me in a vein on my hand that literally GUSHED blood all over the walls and floor! I still have a scar on my leg when Hobbes freaked out too!
Sometimes you just have to figure they won't change. I keep my "confined" lovin to a minimum and make sure they have an escape hatch that doesn't include one of my body parts!

Calvin & Hobbes mom