Our server is deployed on a kube cluster. I'm not too clear on how Helm charts etc.

The only thing that I can think of is that something is not right the the load balancer on the server so maybe some requests coming from an instance on the cluster are blocked ...
Hmm, saying that aloud that actually could be?! Try to add the following line to the end of the clearml.conf on the machine running the agent:

api.http.default_method: "put"