From what you described I don't think you have a problem at all, it is a "feature" in the boxster. If you don't use the car for a week the remote stops working and you need to use the key to get in. This is designed to help keep your battery from going dead. It that is not the case good luck taking the door apart.
As a new owner you may find this link helpful. It is written for the 987, but most of it applies to the 986 too.
http://www.planet-9.com/cayman-boxster-problems-complaints/6951-didnt-read-manual-read.html