I have a E6300 CPU and I got a question is the Stock fan suppose to be stopping? it stops randomly and I have no Idea whats wrong with it. if u need the specs its in the sig.
anyways, no it's not suppose to be stoping at all, does your PSU have enough wattage to support your system? how are your other fans running? try connecting the stock fan to ur PSU directly using a convertor
First, double check your tempatures, my guess is that the DS3 is turning off the fan for short periods of time. Go into the BIOS and disable all the "smart" fan controls.
There's a feature in some system that stops the use of fan, when the cpu is not in use and it's not hot. Energy savings feature and also lowers noise levels. But you can go to the bios and disable this feature and maybe able to set the fan's rpm or just keep it running at all times.