Wrong output folder in a gradle module

I have a gradle project and

./gradlew clean build

outputs everything in the ./build sub-folder as expected. IntelliJ IDEA 2017.1.5 works exactly the same way.

I tried to upgrade and downloaded IntelliJ IDEA 2017.3.1 Unfortunately the behaviour has changed, after refreshing the gradle module Idea changes the output of the module to the ./out subfolder. Even worse, restoring the output folder manually after that doesn't help, because the IDE changes it  back to what it thinks is right when I try rebuilding the module even without refreshing the gradle module before building it.

Is there any configuration parameter that would make IDEA stop screwing up the project structure?