Sounds like you have a hardware problem. Either one of the fans is cutting out, causing the remaining fan(s) to ramp way up to compensate, or the fan speed sensor/motor controller is flaking out and the fan is pinning at full speed when it registers 0. You could probably figure out which by comparing the temperatures; if the temps go down when the fans are way up, it's a bad reading but the fan is working. If the temps go up, that fan is cutting out.
It's also possible that the program you're using to check is having trouble with higher fan RPMs or something, and is showing 0 instead of the correct number; in this case maybe the CPU/GPU is just ramping up during these increased activity periods (maybe Flash in a web page?), and it's just the display that's weird.
Running the Apple Hardware Test disc that came with it would probably tell you if it's bad fan hardware (or at the least won't give a false positive). If it's hardware, time for a repair.