Engine shaders keep recompiling in command line build

In what should be an incremental cook with only project (no engine) changes, we keep seeing thousands of shaders being recompiled. This is happening in our release pipeline where we warm start the cook with a cache of the output of a recent build. We are caching the Intermediate and Saved directories of the project for the warm start. In what should be a very quick cook, we end up seeing the following:

CookOutput.txt (3.4 KB)

Most notable are these two entries:
LogCookCommandlet: Display: GlobalShader.Misc
LogCookCommandlet: Display: ShadersCompiled=822
LogCookCommandlet: Display: MeshMaterial.Misc
LogCookCommandlet: Display: ShadersCompiled=6837

We are trying to figure out where the output of these shaders end up so we can include them in our cache but so far nothing that looks related to global shaders has worked. Does anyone know where the output of these shaders lives and what is tested against to determine whether a recompile is necessary?

Bump. Still puzzled by this.