Home run!! 
by your description, i'm imagining the arcadia as a giant bat with an elysium for a hand. 
Yes, indeed...
That's how it is... And WAM I'm splattered...
on a serious note, it's not a 3.6.8 vp problem, it's been there for a while now.
I know, but I didn't want it to get forgotten

Actually I tried to fix it myself... But this f****** Elysium just won't undock!
Oh... And inspired by this I made a few tests

One Argo - 7 Docking-Bays... Hmmm...
Dock one Argo with another and the other 6 Points... Elysiums (On both Argos)...
Then an Arcadia... Orion to the Big Ship Dockpoint and an Argo on the other... And 6 Argos on the Argo...
Next: Dock an Ulysses with an Ulysses... Looks like some sort of X-Wing...
Now dock an Ulysses with a Leviathan...
Last thing: One disabled Rakshasa...
Command the Argo on the Arcadia to attack the Rakshasa... The whole Arcadia with all the Argos and the Orion is now flyint to the Rakshasa (and attacking of course)...
Now I command one Elysium thats docked with the first Argo to attack the Rakshasa... The whole thing flys to the Rakshasa and attacks...
The double-Ulysses too..
Only the Leviathan-Ulysses Combination doesn't follow this order.. It just flys around... Doing nothing...
Okay.. When the Rakshasa is destroyed, I command the same ships to depart...
Argo-Arcadia-Orion: The Orion stays in space after the Argo-Arcadia warped out...
Argo(with 6 Elysiums)-Argo(also with 6 Elysiums): The Elysium pulls the two Argos out... But the 6 Elysiums on the second Argo stay in space...
But the Orion and the Elysiums ARE still docked with the Warped-Out Arcadia/Argo... So they're docked with nothing... But they're docked...
Confusing... A funny chaos...
Wah.. Look for yourself

EDIT:
Forgot to tell you which ships you should give orders to:
GTT Elysium 12 (For the Transport-Array)
GTT Argo (For the Arcadia-thing)
GTF Ulysses (Leviathan-Ulysses Combination)
GTF Ulysses 33 (The X-Wing Ulysses)
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