Something is overriding config in Drupal - you can see it by invoking drush with and without the flag to include overrides:
$ drush cget system.performance | grep -B1 preprocess
css:
preprocess: false
--
js:
preprocess: false
$ drush cget --include-overridden system.performance | grep -B1 preprocess
css:
preprocess: true
--
js:
preprocess: true
Perhaps we want to turn this config off, but these overrides won't let us.
Where are these config overrides coming from?