My anti-virus allegedly got rid of a virus, but it keeps finding and deleting it from system restore points?

I have AVG and CA anti-virus, and recently had a trojan virus on my computer. It *seems* to be gone, however AVG keeps finding the trojan again within the system restore points or whatever (or at least that's the location it shows when it says where it deleted it from). Firstly, will this affect my system if it's just found in the system restore, and secondly how would I get rid of it from there permanantly and stop it from reappearing in new system restore points?