The fan almost surely runs on 12V.
If you look close at the fan, I bet you'll find a little blue thermistor in there. This device acts as a variable resistor on the 12v input - it's resistance changes according to temperature. It's supposed to regulate the fan speed, but it's really an unwelcome feature IMO. Due to their location, these thermistors are very slow at sensing temperature changes. They lag minutes behind the motherboard and on-chip sensors.
The result is that the motherboard/CPU detect an increasing temperature, the fan speed is set for 100%, but the thermistor hasn't warmed up yet. So for the next several minutes, the thermistor's resistance prevents the fan from hitting it's maximum speed. It takes it's sweet time slowly reacting. The board commands some percentage of maximum, but the meaning of maximum is defined by the ever-changing state of that silly thermistor.
On a modern motherboard, a thermistor in the fan is just redundant and interferes with the board's own control mechanisms. Yet it's common. AMD provided these type of fans with many (maybe most) of their K8 and K10 CPUs. I don't know if they're still doing it.
With modern multi-core, variable Vcore, variable speed power managed CPUs, a load spike can cause dramatic shifts in the heat output of the CPU. It can go from 10W to 80W in the blink of an eye. In that situation, the thermistor is a liability.
For some strange reason, it wasn't until AMD started making these types of processors, where thermistors are the most unneeded and problematic, that they started including thermistor fans. At the same time, they started using 4pin PWM connectors - so they introduced 2 conflicting ways to control the fan, operating in serial. It's very odd. If they had used thermistors in the K7 era, it might have made some sense. On the K8 and later, they're just dumb.
I'm picking on AMD here, but whether yours is an AMD or not, I think you're seeing the same problem.
If it bothers you as much as it does me, then my suggestion is to put a short across that thermistor. On the 2 fans I've done this to, I just desoldered it and bridged some solder across the connection points. On some fans this is easy to do, on others it takes some disassembly.
This makes the fan become instantly responsive, and it always has the same maximum speed available (if commanded by the board). Board says 60%, it runs 60%, period. Depending how the fan speeds are programmed on your motherboard, the accelerations might become abrupt, so that might annoy some. But it's no different than if you installed a fan that didn't have a thermistor to begin with.
When my brother bought a quad-core K10, he had overheating problems in the first few minutes of video rendering. Bypassing the thermistor fixed that.
Later, I ran into a similar problem on a K8 Opteron 280. The problem was made worse because I undervolted it, so it has an exaggerated difference between idle and load power.