Can someone please tell me what the difference is between a Chassis fan connector and a power fan connector? I've been having a minor issue with my mobo and the fans so I think if I knew the difference it might help a little bit.
There is probably no functional difference. The motherboard should have fan spead sensors fo each one and probably has the ability to control them independently. Can you post your motherboard model and manufacturer so we can look up more info?
Ok, I looked at your motherboards manual and I can understand your confusion. The Connectors labeled PWR_FAN1 and PWR_FAN2 are intended to be connected to a fan inside or attached to a power supply. The ones labeled CHA_FAN1, CHA_FAN2 are intended to be used with chassis fans at the top, front, bottom and/or back of your case. Since most power supplies come with sufficient fans built in, you don't need to connect these fans to a power supply, however you can use them as additional chassis fan connectors. BTW, I also noticed that the CHA_FAN1 is a four pin connector so you can use a PWM fan on that connector if you want to.