My motherboard has 4 fan connectors on it (NB, CPU and 2 SYS). All of the monitoring programs I have tried so far can only see 3 of these though (speed fan, mbm, everest, hardware monitor). This would suggest one of the connectors cannot be read, however if I use either SYS 1 or 2 ports for a case fan, these programs show the value up under the third fan. So this proves the connections can be read, but when I connect devices to both ports only one of them is seen. Are there any programs that will be able to use all 4 connectors or not? I'm using my PSU's fan monitor lead in one port, and my side window fan in the other, although I have also tried my rear exhaust fan and side fan in both the ports to no avail.

Did the MB come with a monitoring program? Check in the BIOS system health and see what is being monitored there.