MB Fan ports not working

Recently, the case cooling fan on my Shuttle (SB61G2V3, SmartFan system) stopped running. I replaced the fan but it still did not work. Also checked the BIOS for the SmartFan settings and none of them, even the continuous settings, made the fan work. Finally, switching out the fan cable for an adapter to connect to the standard 4 pin PC power supply got the fan running, but only at its highest setting (noisy, but cool now).

I appears that neither of the 2 fan ports on the motherboard are working. Neither seems to power the fan. Is there something that can be done to reinstate the ports so I can use the SmartFan system again? Or, is there another problem that is making the fan ports inoperative?