I have exactly the same issue (same Noctua PWM fans too). When the computer goes to sleep, the fans turn off. After turn on, the computer runs, but the fans do not. Here's the interesting part, the fans do turn on, albeit for 3-5 secs after wake up, but then turn off. And remain off.
Here's what I've done so far. I installed the Intel XTU and fired up the CPU to 100% for five minutes hoping that it may be a temperature issue. Nope, the computer ran at full throttle and did not turn on the fans.
I changed the settings in the (visual bios) to receive 100% input from the CPU and <60% duty cycle. Ok, so here's the strange thing. If you change the duty cycle on a case fan, all the fans change. So now the CPU fan as well as the case fans run at whatever setting the fan is!
Next thing I did was turn the fans to manual. Again, changing one fan changes all the fans!!!!! But, the fans do turn on after sleep. However, this is not ideal as now the fans always run at whatever speed you've set them at.
What I want is a fan profile path where when the computer is cool the fans spin slowly and when the computer gets hotter, the fans ramp up. Not a single fixed speed.
PS - I've reset the bios - no difference.
Update1: When using Noctua fans, Duty Cycle must be 60% or greater!! Then it seems to work as it should (at least on manual mode).
Update2: Don't mix PWM and regular fans (even from the same company) on Intel 87 series boards! Tested it and it does not work properly.
Update3: Auto mode definitely does not work. If you set the fans to auto, put the computer to sleep, the fans will not resume after wake up. It does, however, in manual mode >60% duty cycle.
Update4: If you set the case fans to manual, but keep the CPU fan in auto mode and put the computer to sleep, the manual mode fans will spin, but the CPU fan will no longer spin regardless of load or temperature of the CPU.