Did you run ECS on a custom AMI, or use the stock one?

We've been running with vanilla EB + ECS for months and haven't seen this at all.

From an outside perspective, it sounds like the primary issue you referenced here (the agent disconnecting) could have been due to a mismatch in configuration between the agent and docker, or maybe just a permissions issue. IIRC, the ECS agent tries to clean up containers every few hours so perhaps not being configured correctly caused it to get stuck?