Hmm. you say she wasn't like this before.. is it possible that maybe a visitor to your place did something that scared her?
In my opinion (and I could be wrong) i don't think that sort of behavior is because of either of your two boys..because it's more of a people phobia, not a cat phobia.

I have 2 boys and a girl as well.. And Eliza, my girl, is the same way, but because she was ignored when she was younger by my in-laws and whomever had her before they did.

It's taken a lot of time to get her accustomed to me, she is slowly allowing herself to be picked up, and is slowly learning that my husband and I aren't going to get rid of her like her past parents did. She is still scared of strangers, maybe she thinks that she'll be leaving again...

I would however, take her to the vet to make sure that everything is ok with her, maybe she's just sensitive to the touch (i know Eliza and Bach are real sensitive on their backs, and will bite me if i brush there..) Once that comes back ok, and i'm sure it will... the only advice I have is to take it slow, and on her terms, and get lots of whatever treats she likes best.. and catnip.. and slowly she will realize again that you aren't the bad guy, but a great place to get lots of attention!