Often, when I need to get from point A to point B, and both have "Phase Stabilizer Node" in their gravity well, the ships will choose REGULAR star-lanes (using more than one jump) instead of taking the single phase-stabilized jump.
I did a few hours of testing using the saves provided above and what I found is a bug that is definable and repeatable. The Phase Stabilizers all work as they should except for the last planet or planets that you colonize. Eventually even they work correctly, that is the only part that I was unable to pin down. I tried and eliminated half a dozen possible triggers . The closest I can come to a conclusion is that after a certain amount of time (somewhere in the neighborhood of 10-15 minutes) they begin to work correctly.
Nypyren confirms this with his update, which got me started on this investigation.
If you use Autosave-20 above (Reply 4) and follow the instructions, you find the fleet on a world that appears to be newly colonized. It already has a phase stabilizer constructed on it, so there is no need to select the Marauder and if you attempt to phase jump off, exactly what Nypyren says will happen does happen, its jumps 3 times to get to the nearest phase stabilizer and goes to its final destination from there.
Annatar11 and Kitkun both confirm this.
So a Phase Stabilizer built on a newly colonized planet will not work for outbound jumps, eventually it starts working. It started working for Kitkun after she built two more stabilizers, but like I said this wasn't repeatable.
The same bug appears to affect the Antorak Marauder's Level 6 ability to create a temporary phase stabilizer node (assuming you don't give the Marauder different orders afterwards -- this cancels the effect).
This does not appear to hold true, it again has to do with the planet. If you take a Marauder to any planet that has been colonized for awhile, or any uncolonized or enemy world. It works perfectly 100% of the time. However if you colonize the world that it just seconds before worked, wait for its cooldown and try again. It reacts the same as a “Phase Stabilizer Node” it exhibits the buggy behavior. It appears that to the game, they are the same, whether its a physical satellite node or a temporary node created by the ship. It shows up the same in the info card.
I've noticed this in every version, aswell... there may be a hard cap on a maximum number of phase stabilizers that work together as a group that needs to be raised.
I was unable to confirm or reproduce this. I jumped from every stabilizer on that map and never saw this behavior. I am not saying this isn't a part of the bug. But if I had to guess, I would say that because of the way the bug is, always at your newest planets and probably where you are most active it could easy appear this way.