First off the system fans wont be monitored unless plugged directly on the motherboard with these little connector...
Second off yeah, more system specs could help.
The cpu fan should start spinning as soon as you open the computer. Try this, start the computer with the side open and as soon as you open up the computer give a little spin/flick/whatever on the fan see if it might start it. You might have a sligly defective fan that gets (stuck) between two steps. If so you should change it.
You should also make sur the heatsink is properly mounted and well secured on the motherboard, you should be able to move it or rock it when its in place.