There may be a fan cycle control operating one fan motor. If you do see this, change the wiring to cycle both fans.
There also may be an ambient sensor mounted above or near the fans. The ambient sensors are junk (in my opinion) and should be cut out and a fan cycle control installed.
If there is a headmaster in the refrigeration circuit and a fan cycle control then the headmaster is probably bad and wasn't taken out.
If you can, remove the headmaster and use the fan cycle. If you can't remove it then pinch off the by-pass line. Watch your flow pattern and don't pinch off the wrong liquid line. Please don't just pop the nitrogen fill port tube, some of them will leak refrigerant through the tube.