What should I do if I'm unsatisfied with my recent roof replacement?
As a contractor, I will share with you an approach that may help.

First of all, you need to document the current leak with pictures, dates etc. When you communicate with your roofing contractor, be calm and polite, explain precisely the problem and ask to witness his/her inspection. Explain that since this is the second occurrence of the leak since the new roof installation, you are concerned that water may have compromised the insulation and framing and is a potential cause of mold or rot and must be addressed. Tell the contractor that you insist on having an infra-red scan inspection of the effected area to detect any current moisture in the cavity before any more repairs are made. If the roofer is not willing to do this, tell them that you are terribly sorry we could not reach a mutually reasonable solution. Calmly but firmly state that you now have no other choice than to have this scan done yourself and that subsequent repairs will be made by another contractor and the total costs will be litigated in a civil action against him/her. Carefully and concisely summarize your conversation and send a letter with your demands via certified mail immediately after your meeting. If the contractor does not respond favorably after written notification, contact the BBB, and licencing bureau of your town or state. If none of this induces the contractor to act, proceed to having another contractor do the scans and repairs. Follow through with civil action, usually small claims on both the contractor and his/her insurance company.