Unless you need speed regulation, try to keep fans - especially fancy LED fans - off the motherboard headers. The headers are usually designed for smaller fans and have a limit on the amount of current they can supply, and larger case fans can quickly over-run those limits.
Of course if the fan only has a 3-pin connector, then its easier to plug it into a motherboard header. Also, see if there's another header on the MB that you can plug it into instead of the NB header.