I'm not sure why you would want NOT to run with two fans, but that's not your question. Your problem is in HOW the Splitter is used.
All fans send back to the host header on Pin #3 a speed signal that is 5VDC pulses, 2 per revolution. The header counts those to get a speed reading. But the header can NOT deal with speed pulse signals from TWO fans at the same time. It causes wildly fluctuating wrong readings and errors. So any Splitter or Hub will send back to the host header the speed pulse signal from only ONE of its fans, and ignore the others attached to it. The simplest way for a Splitter to do this is they omit the male pin in the #3 position in all of the output connectors except one. So when you use a Splitter, you MUST plug one fan into the only output that has all FOUR pins present. If you leave that connector unused, the header get no speed signal and believes the fan has failed.