The way it is supposed to work is the following:
Unexplored jump points aren't bound to a new system until you explore them. When you explore them, Aurora randomly chooses a system ID (where the number of possible system IDs is the max number of systems we're talking about). If there is no system with that ID, Aurora generates one and uses it as the target system; if there is a system with that ID it uses the system in question as the target system. If the target system has any unexplored jump points, then it randomly picks one as the other side of the jump. If the target system has no unexplored jump points, it creates a new "dormant" (not sure if this is the right name) jump point and uses it as the other side of the jump. In Starfire, these new jump points were a special type called "hidden", which was technobabble to explain why they weren't detected when the system was surveyed. Hidden jump points could only be detected by going through them or watching someone go through them, not by survey. In Aurora, the dormant jump points are normal jump points and can by detected by (another) survey after they've been created (by a ship going through them).
So the way it's supposed to work is that the odds of generating a new system are roughly (Nmax - Nexplored)/Nmax. Whether or not the mechanisms are bugged is another question - based on the descriptions in this thread it sounds like they are.
John