I don't get why people uses such a low wattage PSU, I understand that "yep" this will be enough moment, but why have just enough? Should always get more then what you need, this way the wattage will not be an issue later one down the road. Perhaps my definition of low wattage is different from everyone else, but 550W just seems too low to me. I'd try aiming for 1000w or more PSU, but that is me.
Perhaps the cpu is being starved of the needed power due to the GPU eating most of the power when it is working. Remember when the PSU approaches the maximum output, it get very unstable, so that 550W PSU is not guaranteed 550W output rating, it would probably be safe within 400 or maybe 450W range. Perhaps that is too generous, so I don't know. I cannot say for sure if it is the PSU, but it could very well be it.
Have you ever tried plugging your computer into a kill-a-watt meter? This should give you the total power consumption throughout the process.