As a relatively new user, I understand your question. You may also be wondering why the game update affects MQ. While I am not a programmer I have gathered that MQ uses those events that are processed on your computer and takes advantage of the codes that your computer sends to the EQ server by modifying them between the server and the interface. Sony changes the way the codes are sent or their decoding filters with almost every update. This means that MQ will not work with a new game .exe until the files are reconfigured in a new compile.
Be careful with using MQ and sending petitions, complaints, or screen shots as anyone looking at those can see you are using. Those items that are totally on your computer such as imitating key strokes cannot be seen by the server. Moving from point A to point B faster than SOW or SOE or innate run speeds are also very visible to GMs that have access to the logs (they look when there is a complaint) or when they are in zone. Those commands that are labeled as active hacks are the ones that are visible to others and can get you banned or suspended by Sony.
Good luck.