Script of previous area still running Options

[Baronius]

In my BG1 mod, the party is AR3300. Then as a result of a dialogue, it gets teleported via LeaveAreaLUA to BW0506. (BW0506 isn't an indoor area of AR3300, it has no travel regions at all, by the way.)
There is a battle in BW0506, and you have to kill both main villains to be able to leave the area. When this happens (their Death Variables are one), you can use a wardstone (give it to a guardian), who will teleport you back to AR2300 with LeaveAreaLUA. In AR2300, a cutscene script with a dialogue should start (which is also triggered by Dead() functions, so if you have killed both of the villains).

My problem: the script of AR3300 (Beregost) is still running in BW0506 (which is a hall), because AS SOON AS the second villain dies, the cutscene (basically a dialogue) in AR3300 is triggered, of course in a black screen. When it ends, the screen returns to BW0506. (So the wardstone isn't used; the party doesn't have to be teleported to the new area to trigger the cutscene in THAT area).

I added BW0506 to mastarea.2da, so its script is running on the top. But AR3300 is also in mastarea.2da, as an area of the original game. This may not be related with the script problem, but I thought it would help (it didn't).
What can the problem be? How can I entirely "leave" an area, so its script won't run anymore?

I could solve it (I could set a global variable when the wardstone is used, and use this as a trigger for the cutscene), but I want to sort out the original problem; I would like to know how those area scripts work, because it seems I am not familiar with them