Ok, I don't know what precisely is going on, but it sounds strange.
What I can do, is give a small fix for the current weirdness.
Download and copy
this, put it in the scripts folder and load the game save. It SHOULD kill all SY and EQ's in SB. Save game, then get the newest verion of the script. This should recreate the stations. If it doesn't, I'm going to have issues.
I don't know why ya'll are having problems, but something came to mind.
Look in the scripts folder for the following file names:
setup.jakesnake5s.factory
jakesnake5.y.stations
jakesnake5.position
lib.Disruptor.Factory.List
lib.Disruptor.Factory.Stop
lib.Factory.Checker
lib.Y.Disruptor.Fab.setup
lib.undockall.ships
setup.Disruptor.Factory
If any of those have 2 files, one with .xml and one with .pck, delete the .xml. It doesn't belong there. (Though, it shouldn't be causing any problems).