I have one (Kiddo) that's a bit skittish also... it can't be attributed to bad experiences in the past because this little guy was born IN my house, so I know that he's been treated kindly from day 1.  His mother is sort of feral, you can pet her sometimes, but she's pretty skittish and lives outside- I also have known her since she was a kitten and know she was never abused.  She's lived inside from time to time but just chooses to live a more feral type of lifestyle.  Kiddo, on the other hand, it not allowed outside.  He still tends to jump when you reach out to pet him and he's the least likely to want to be held, but he does love to sit on my lap.  But his brother from the same mother is the most social cat you'll ever meet.  Anyhow, my point is, I think every cat just has a very different and unique personality, maybe some of it is genetics and having feral blood, but mostly I think some cats are just naturally a little more skittish- a "fraidy cat."  I wouldn't worry or go out of your way to make her trust you- just let her be who she is- without knowing her background or anything, I would guess that this is just a personality trait. 

As for the bad breath, I've never really heard of that, but I would take Robert's advice.

It's been a couple months since you posted this- how are things going?

Scarlett is better as far as being skiddish with me. She tolerates being held for kisses but it doesnt last long. I went to the vet today with Suki and told them my concerns for Scarlett, not only is her breath bad but she has a huge appetite and gain alot of weight. So starting tomorrow she is on a diet. Its hard for me to not feed her when she is begging me at 4am. LOL but I do plan on taking her to the vet for bloodwork to be sure her thyroid isnt wack and her gums are ok.

Thanks for the input. I believe your right each cat does have unique personalitys and we need to let them be who they are and love em every chance they let you.

Glad you're headed to the vet... I've never heard of a cat with exceptionally bad breath!  I'd be interested to hear what's up if you find anything out!