I've just thought of something interesting. Remember how Rush was held on the alien ship for longer than Chloe? His skin never changed, why would the aliens only do this to Chloe and not Rush?
I have a theory in the works:
Rush's skin was indeed changing but he didn't tell anybody, so he used the chair to cure himself. Considering the amount that Rush lies, he decided to use the chair on Chloe, but edited the program enough so that it didn't kill the alien infection. I'm not sure why he put her in the chair as of yet, but maybe the chair is responsible for why she has become good at mathematics (and not the alien infection) and Rush is just using her so that he doesn't have to do all the work.