From my understanding of the Docker issue (and I am in no way a Docker expert), the issue is that, even though you may have told it to shutdown a particular Container, *something* is still running. And it's that still-running component that is getting corrupted.
It's not like the entire Container is "really" up and ok. It's some "leftover".
The best you can do is probably the following:
1) While TTE is running, export and archive all Entities about which you care.
2) Shutdown TTE as Admin, then wait a few minutes.
3) In an Admin CLI window, issue the command: docker-machine ip DockerMachinePTC.
4) Confirm that the return of that command indicates that no IP is assigned to DockerMachinePTC.
5) Attempt a Shutdown / Reboot of your computer.
6) If you get a Windows warning saying that Virtualbox or Docker is still running and do you want to force the shutdown/reboot... you're probably about to run into the issue.
At that point, I would probably cancel the shutdown / reboot, boot TTE back up, and Export all my important Entities *AGAIN*, just to 100% make sure that I'm not going to lose anything. Then follow the procedure above and force the shutdown / reboot if necessary.
Fortunately, uninstalling / re-installing TTE isn't that long. Recreating lost TTE Entities? Now *that* can be time-consuming.
Once again, sorry if this really is the issue you've run into,
Jason