mines a similar problem, 4 x Noctua NF-F12 PWM 120mm fans, all the same, but run at different speeds depending on fan header used.
in Xpert fan 2 latest version;
CPU_FAN allows min 13%
CHA_FAN1 min 70%
CHA_FAN2 min 90%
CHA_FAN3 min 46%
if i change fans round to different headers... same result.... so its the Fan headers that are doing something crazy........
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Corsair H100 4 x 120mm Noctua NF-F12 PWM (2 Push/2 Pull) | Xigmatek Gigas Black Case