Basically, "just" means "a short time ago".
How much time is "a short time ago?" Since time can be relative, that depends on the situation. It could be a matter of a few days. For example, if I moved to New York three years ago, I might say:
I had just moved to New York when my car was stolen.
That's a reasonable way to explain the situation, if my car was stolen during my first week in New York.
On the other hand, in a scenario like yours:
I had just checked into my hotel room when the phone rang.
I would probably assume that refers to a much shorter span of time – probably less than about 15 minutes – because we typically only stay in hotel rooms one or two nights.
So, when we say:
I had just done X when Y happened.
that means X had not been underway for very long when Y occurred.
I had been living in New York for about a year when my car was stolen.
I had been in my room for an hour or so when the phone rang.
In other words, the expression "just started" is much like the expression "almost finished" – one means "not long after something has begun" while the other means "not long before something has concluded." So, for example:
I had just started eating when I felt a pain in my stomach.
In that sentence, we can guess that most of the food is still on the plate. On the other hand, if only a little food is left on the plate:
I had almost finished eating when I felt a pain in my stomach.