Fluentd unable to read logs from all namespaces
Million dollar question - are you running your fluentD as a DaemonSet?  If not, there's a chance that fluentd simply isn't running on the node where some containers live.
Otherwise, my best guess is, it's missing permissions to read from all namespaces, especially since you mentioned you haven't attached a ServiceAccount to it.  If you used a public FluentD Helm chart such as this one, try making sure you're deploying it with rbac enabled, i.e.:
rbac:
  create: true

serviceAccount:
  create: true

It'll also help if you post some logs from your fluentd container.