Edit: To add, this happens on all ships for me, and I'm on Steam
The Summon Jumpship interactable in the tower isn't working like it should, the ship cannot be seen for half a minute, and then you notice its flying super slowly towards the hanger bay, but before it arrives the screen turns back and the ship vanishes. Both Summon Jumpship interactables do the same thing.
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I just tried both of them and they work fine for me. Quite the snappy reaction to being summoned, in fact. Perhaps it's something specific to whatever ship you have equipped? Try switching ships and see if anything changes. Weirder things have been known to happen; especially in this game.