Comment 35 for bug 1290110

(In reply to Guenter Roeck from comment #8)
> Something in your system configuration is wrong. Usually this comes from the
> BIOS, so you you might want to check if there is a BIOS upgrade available. It
> looks like the system believes that your CPU is freezing and therefore runs
> the CPU fan at minimum speed.

As I recall the IT87xx chips need an offset programmed by the
BIOS in order to return "sane" temperature values from PECI sources.
Without the offset, the driver returns the thermal margin as a negative
value (-47°C here would mean the CPU runs 47 pseudo-°C below its
critical temperature.) This matches the values returned by coretemp (99
- 47 = 52). This would justify the low fan speeds.

The original poster could try setting temp3_offset to 99 (in the right chip section of sensors.conf, followed by "sensors -s" as root) and see if it makes the system behave differently.