I have an MSI 970A-G43 motherboard and I have two Rosewill RFX-120 fans connected to the sysfan1 and sysfan2 connectors in the motherboard. The fan connected to the sysfan2 port is not being detected by the motherboard although it is receiving power since it is spinning. The fan connected to sysfan1 is being recognized by the motherboard and is labeled as "system fan 1" by the msi's software "control center". I also used the app "CPUID Hardware Monitor" to make sure that the problem wasn't just with msi's app. Here is a screenshot of both apps.(click on the image to see in full size). In the picture, only two fans' RPM is being detected(CPU fan and the one in sysfan1). The fan connected to sysfan2 is seen as having an RPM of 0 even though it is rotating.
I also used a fan speed control app to confirm that the fan being monitored was the one in sysfan1 connector. I used the app to stop the fan that was being recognized as system fan and indeed it was the fan connected to sysfan1 to that was brought to a stop. This also means that the sysfan1 and sysfan2 connectors are not synchronized or meant to be detected together as one fan.
The only difference in the the sysfan1 and sysfan2 connectors is that sysfan1 has 4 pins and sysfan2 has 3 pins. However, both fans are 3-pin fans meaning that the additional pin in sysfan1 is not being used and thus should not make a difference.