During my escapades, I ran into a problem with the fans myself, when I used the stock ECU to control the fans, it would never turn on, so I rewired the fan relays to work through the Autronic. Wanna know the root cause.... LOL
Anyways, even though the NA Subaru Temp sensors look the same between the NA Legacy GT and the STI, they are completely different. They are both 3 wire types but the STI one didn`t work properly with the NA Fans.
Root cause: STI Water Temp sensor not working with NA ECU. In your case, I don`t know which ecu you`re using or water temp sensor you`re using, but it`s a simple thing to test.