Configuring "extraArtifactVersionKeyRules" with a file in a sub directory:
extraArtifactVersionKeyRules(file("gradle/refreshVersions-extra-rules.txt"))
This works just fine using Ubuntu.
But when running in Windows, the extra rules are not evaluated (for me).
file("gradle/refreshVersions-extra-rules.txt").exists returns true - on Windows.
Workaround
Moving the "refreshVersions-extra-rules.txt" file to the project root directory, solved the issue for me.