I am pretty sure, as far as I can tell over the internet, that this is a temperature problem, like calza stated before. Your components heat up during load produced by the game you are running, and getting hotter and hotter. As soon as they reach a certain temperature your CPU or GPU clock goes down to prevent damage from overheating, this means that your system will now run a lot slower. As soon as they cooled down a bit, they start to run at full clock again, till they reach a hot temperature again - then the circle repeats.
That's what heat throttling means. The reason why it has been running fine before is propably dust which blocks the heatfans so air can no longer go through them