I suspect I know what your problem is here.
You've based the mission around (0,0,0) right. So all the numbers range from high positive values to high negative values. The problem is that the random functions don't deal very well with negative numbers. The game figures out what the difference is between the high and low value you entered by doing this.
diff = high - low;
if (diff < 0)
diff = 0;
The game then takes a random number between 0 and the value of diff and adds that the low number. As you can see that calculation will be thrown completely out by the inclusion of negative numbers.
You have two choices.
1) Change
rand-multiple
- -1000
- 1000
into
+
- -1000
- rand-multiple
-- 0
-- 2000
2) Simply pick up and move everything in the mission so your centre point is (1000,1000,1000) or whatever.