You have not provided enough info for me to tell you this is your cause, but check this detail. You can always plug both 3-pin and 4-pin fans into any 3-pin or 4-pin mobo header. MANY mobos now use only 4-pin headers, but many of those can be configured in BIOS Setup in different ways. That includes possibly setting a header to use the older control method for 3-pin fans, Voltage Control Mode (aka DC Mode).
Now, if you "mis-match" a fan type with a header type, one combination has a particular limit. If you plug a 3-pin fan into header that uses only the newer PWM Mode method to control, that fan will always run at full speed. If your mobo's headers offer the appropriate configuration settings, you can solve that by changing the header's Mode to Voltage Control Mode (aka DC Mode). So, IF your fans are of the 3-pin type, check in BIOS Setup whether each fan header is configured to use this older Mode. If you change it, remember to SAVE and EXIT. But while you're in there, verify that each fan header also is set to use the default automatic control system, and NOT set to a fixed speed or to full speed / max cooling.