I was using an afterburner fan profile and noticed my 3rd fan (fan right over the pcie power connectors) was spinning noticeable slower than the other 2 fans. I thought there might be an issue with afterburner, so I went back to default fan profile and noticed the same thing.
I notice another issue that is related. The 3rd fan will not spin at a low speed. I can set the other 2 fans to run at 340rpm, but the 3rd fan will vary constantly from off to on. It's almost like the other 2 fans are pwm and the 3rd fan runs on voltage. Other people have reported the same thing, so I think this effects all cards.
Can you check your card? Run a heavy bench and visually look at all the fans. You will see that the 3rd fan runs noticeably slower than the other 2.
You will also notice fan 3 is not listed in hwinfo.