HELP! My Pirate Bases disapear - dont know why!

[Cpt. Jack Sparrow]

I have a little problem with my mod:

Some of the Pirate Bases in my Mod-Universe disapear after a while. But i fail to undestand why because they are already gone by the time i first visit the Sector. There is nothing in those Sectors that could kill a Pirate Base. And the Nebulas i have placed to hide the Bases are not hull or shield damaging nebulas, so that's not the problem.

I have already set up a map with player ships near the bases in all those sectors to check if they are there at the start, and they are! So what the hell is going on?

Any ideas?

The only Scripts runnig are those of the bonus package and pirate bases rebuild is on.

[3iff]

There is the possibility that local race patrols visit the sector and destroy the base...then move on to another sector.

[Cpt. Jack Sparrow]

Race patrols are disabled. So the only ships in the sectors should be those i placed there.

The sectors i've had the problem so far are always far of sector's with little to no traffic.

[Harlock776]

If you start a new game in a custom galaxy then the npc M2/M1 will attack any and all pirates immediately but if you start the game with story mode then the pirates are left alone. For example the argon M1 in sector ore belt will just go to work on that pirate base behind the gate as soon as you start in a custom galaxy with no story but it will always stay far away when using story mode so the player will be able to complete the ore belt mission.

[Cpt. Jack Sparrow]

Does that count for Pirate Bases in Sectors without M1/M2 Ships to? I mean they would have to fly there to do the Job! Never seen anything like that happen...

But for the Case:
How do i start my Galaxy in Story Mode? I don't think that is possible because most of the Sectors, Stations etc. required for the Story to work are not there.