Pierre Wilén wrote:
> I have researched this and there does not seem to be any setting for this
> in the bios. I can only see the current CPU-temp and the fan speed in the
> bios.
> 
> The FAN-section in the manual says the following:
> "CPU Fan and System Fan: CPUFAN and SYSFAN
> The CPUFAN (CPU fan) and SYSFAN (system fan) run on +12V and maintain
> system cooling. When connecting the wire to the connectors, always be
> aware that the red wire is the Positive and should be connected to the +12V.
> The black wire is Ground and should always be connected to GND.
> FAN_MCM is a switch that is used by high-quality fans to monitor the system
> temperature and will automatically adjust according to the environment."
> 
> Does this mean that it only runs based on a hidden, preset, threshold?

It is probably based on a thermally-regulated part that will let power 
flow when it is hot enough.

> I have also set a cpu and chassi max temperature threshold (powerdown if
> things get too warm I guess?) - but this should be unrelated?

Probably unrelated.  But you really want your cpu to stop your firewall 
it it reaches this temperature?

> 
> Connecting the fan to a regular molex connector works, so problem is
> "solvable", but as described when connected to the sysfan 3-pin
> motherboard connector it stops running after boot is completed.

Personally, I don't see that as a problem.