It did not fix the issue. Here's what happens: if I tell the Gray Goo Armor to stay on the ship while I'm on the crew quarters space, she won't show up in the crew menu. If I do so on literally any other place on the ship, she'll show up on the crew menu once I go there and check. I thought it might be because I technically have a 'full' crew, but doing this with a new save file and 1 'real' crew slot results in the same thing under the same circumstances. Save file attached, with gray goo armor, for reference and testing.
Okay, I see what has happened. This is only a visual bug that's not something I can easily fix with how buttons work at the moment without rearranging how crew member buttons are generated.
Essentially, when you go into your inventory, the game takes a snapshot of what your buttons are (including to what functions they lead to). So since you're character is on the crew quarters tile, clicking on it will normally not show the Gray Goo Armor since she hasn't been brought back into your crew yet. When you access your inventory to interact with the Gray Goo Armor, the game will save that list and reload it once you get back out of the inventory, giving you the same list of crew members prior to accessing inventory. Of course, when you access the inventory when not on the crew quarters tile, a different set of buttons will be saved, and stepping onto the crew quarters tile would refresh the list as expected.
To get around the issue, at least for now, you can go into the crew menu, back out (to reset the list) and go back in, and your Gray Goo Armor character should be present to be interacted with. So functionally the flags that control when she is or isn't present is working as intended, it's just the buttons that are reloaded in are not "up-to-date" with your new crew member list. Apologies for the inconvenience.
Edit:
The softlocking issue is also related to the button saving aspect of the UI. I've brought this up with the team to see how we can better streamline the button handling when swapping between different menus. My advice for now is to not use any of the side buttons while you are in the inventory or interacting with an item/character from the inventory. The softlocking is caused because accessing the Menu or Data may take a snapshot of buttons that aren't there, so when it reloads, it reloads nothing--and because the state it saved isn't the main text screen, the navigation buttons aren't enabled.
If the softlocking does happen again, and if it's possible, access your character's appearance (via the bust window). Exiting out of the character appearance screen should go back to the main text screen and regenerate/enable the buttons again.