This repo has a simple reproduction of an issue shading shapeless.
There are two subprojects, one of which is configured with .inProject.inLibrary and the other configured with .inAll
You can assembly them both with sbt assembly
Then, if you check the jar files, you'll see that the "fails" project isn't fully shaded, but the "works" project is.
[shading-repro] jar -tf works/target/scala-2.11/works-assembly-0.1-SNAPSHOT.jar | grep shapeless
shadeless/DefaultMacros$$anonfun$shapeless$DefaultMacros$$methodHasDefaults$1$1.class
[shading-repro] jar -tf fails/target/scala-2.11/fails-assembly-0.1-SNAPSHOT.jar | grep shapeless
shapeless/
shapeless/ops/
shapeless/ops/record/
shapeless/syntax/
...