ELK stack not grabbing all logs

I’m still fairly new to rancher and am having trouble with connecting certain services/containers to my running ELK stack. I configured the elk stack according to the rancher-blog post. My issue is that when I create containers from my hosts using docker run commands, the logs are being pipelined and I can see them in Kibana. If I create the container by using the services tab in the UI though, the logs are not showing up. I have tried creating them with service links to logspout, logstash-collector, as well as without a service link.

Any ideas as what I should be doing? Thanks!