Ok so you could have lead with the fact that you had customised the bootstrap script 
These modifications create three organisations and then attach the user to the last one from the looks of it. So essentially you have every new user added to the last org, but each time you run it you are generating three orgs (two which aren’t used).
Now this is a docker install I’m guessing? So this script is very specific to the docker compose setup and really should only be used once.
If you want to add more orgs and users you should use the REST API (it’s what this script does, but it also does a whole lot more and is designed to stand up a very specific docker demo / QuickStart). I wonder if fiddling with it caused the problem - perhaps assigning a duplicate org ID to your second user when you modified it messed things up.