I had a similar problem and in my case I found that docker was launching mender before all required systemd services were up. In the end i configured docker to not start mender containers on boot and added my own mender systemd service to ensure the required system services were up before launching mender-server. See below for systemd service I created. Obviously your setup will be different so change the necessary values to suit
[Unit]
Description=Mender docker embedded image upgrade services
Requires=docker.service
After=docker.service systemd-user-sessions.service
After=network-online.target network.target
[Service]
Type=simple
TimeoutStopSec=300
User=mender
WorkingDirectory=/home/mender/applications/IwMenderServer/production
ExecStart=/home/mender/applications/IwMenderServer/production/run up
[Install]
WantedBy=multi-user.target