It happened after just a few hours of first being used. I refuse to go through the trouble of manually fixing the timing (because I shouldn't have to).
I'm no audio engineer but what you describe is I believe is called 'latency' which is particularly affected by computer power and what else is running. A search here (for latency) gives about two hundred hits, and google closer to two million ( for latency + midi). That the problem appears after running for some hours suggests other programs are running. Check the Task Manager to see where your CPU is being used.
Others members will no doubt have more to offer and almost certainly will be asking you about your computer specs -- a core i7 or a pentium 3?