I'm glad it's working for you. But I believe your problem was that you somehow had path.config set in your logstash.yml file. And this was fixed because you started from scratch with a default set of config files. Of course it's impossible to tell now.
But for any future folks having a similar problem, I'll spell it out:
Logstash reads logstash.yml first. If you have path.config set, you will not be using pipelines.yml. Check logstash.yml first, to see if it's loading a different pipeline than the default.