X48 DQ6; Fan2 much slower after BIOS flash

I have a GA X48 DQ6 and a Coolermaster Cosmos 831 (first edition, no WC holes or cross fans mounts etc.)
with a total of 5 fans in (1 rear exhaust, 1 top exhaust, 2 bottom intakes, 1 hdd fan; all 120 mm), the 2 bottom
intakes and the top exhaust are all connected to the motherboard 3-pin connections, the bottom intakes
to SYS_FAN2 and PWR_FAN and the top one to SYS_FAN_ATX_12V or something like that. They were all happily
spinning on about 1600 rpm on the F6 bios. Out of sheer boredom I decided to flash my mobo today and now
I see one of the bottom intakes spinning at just 700 rpm in the BIOS, and noticably slower when looking at it
compared to the other intake next to it as well. Why did they do this? I tried SpeedFan but it can't set it higher
than 100%... Anything I can do to remedy? It's well retarded.

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  1. EDIT: Typo, make that coolermaster stacker, not cosmos :-)
  2. Oh yeah, another thing, the fans spinning at full speed are all 3 pin and connected to 3 pin connectors, this one is 3 pin connected to a 4 pin connector, so maybe I need a 4 pin fan here? :p
  3. Info from GB global service:

    CPU_FAN connector needs a CPU cooler with four wires where the PWM modulator is included in the cooler. The mobo senses the CPU temperature and managing the pin 4 signal, the cooler's fan will automatically be increased or decreased, following the CPU temp. Fan's rotation feedback returns via pin 3 for BIOS alarm feature.
    SYS_FAN2 connector needs any fan, with three or four wires (don't care) since the speed is controlled via on-board PWM controller that supply pulse-width-modulated 12v for the fan via pin 2.
    So, if using a four wire fan, its internal PWM is locked to full speed (this explain that fixed 5v on pin 4).
    This time, the mobo senses the North Bridge (in my case the P35) temperature and will increase or decrease the speed of the fan connected in this socket. Feedback is sent to pin 3 for BIOS alarm purposes.
    SYS_FAN1 and PWR_FAN are three pin socket with fixed full speed fan. No controlled rotation at all from the mobo. Rotation feedback also monitored via pin 3 only for BIOS alarm purpose. But no, NB header has power only. No sensor or control
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