@SimonQ Without complete knowledge of your setup, we can't exactly tell why redis started with the proper database one time, and not the other time.
I will say that Redis is designed to be running in the background, so there should be no ill effects from doing so.
If Redis is already running in the background, you can invoke
redis-cli shutdown (as far as I know), but this is not recommended. See below.
If you're running Redis by invoking "redis-server", then it probably assumed defaults for the location of the database file, since you didn't specify a config file for it to read.
Are you running Linux? The recommended way to start and stop redis is using
# As root...
$ service redis-server stop
$ service redis-server start