In our assembly there are currently 4 configurations that have been created. We display one of the configurations and on save except for the shown configuration other configurations get deactivated. Is this a standard behavior? If not how to make all the configurations active upon save.
That sounds like normal behaviour. Only one configuration should be active at any one time. The configuration you save it in will be the one it opens in, unless you tell it otherwise in the open dialog box.
If you want multiple configurations showing at once, you could put multiple instances of your assembly in a new assembly and set each one to a different configuration.