The encryption key problem is typically because you ran PSU on the same address\port and then ran the server again on the same address and port but in a different way.
For example, you had it running locally on port 5000 and then you started it up in docker on port 5000 and it used the same cookies. That’s when you’ll see that warning\error. Usually, I don’t see any side effects of this and PSU behaves.
As for losing the config files, that shouldn’t be happening and is unrelated to the “unprotecting cookie” problem. We recently made a change to our dockerfile and updated the docs about persistence so this could still be an issue. More info here: Issues running in Docker what am I missing - #8 by rsrychro
Is there any way you can share the dockerfile or command line you ran to configure you instance?