Oh! So HWMonitor is has read and shows a minimum fan speed of 0, even though the fans are now running? (And HWMonitor has caught this for two fans?)
If it was just one fan, I would ask if it is plugged into the "PWR_FAN" header, because that can cause weird readings. But, with two fans, I doubt that is the case. I had a friend who did that, and his fan speed readings would jump between 1000 and 675,000.
Unless you can catch one of these fans "acting up", I would chalk it up to just weird RPM readings. Try downloading Speedfan, it too logs read-outs. If it gives you the same results, but the fans are still running properly, then you know it's not just a software issue. How to fix it from there, I do not know, but keep a close eye; it might just be a minor inconvenience in the long run.