So I just tested out NJ's save and found out some interesting things, that match what
@lazyNiks reported.
If I go into the cell, I immediately start sinking - plus I can see a bunch of physics items falling infinitely in various spots. If I then load into a completely different save with a different character that's in HQ, that character has the problem too! So the issue is the way the cell is being loaded into memory. If I exit the game, and load back up into my character, the sinking is gone.
Also, if I make a new copy of NJ's save without any other mods but WSFW, SS2, and Chapter 2, exit the game, and then go to HQ - the issue doesn't occur. So there's definitely a mod conflict going on here that's baking something into the save file that gets cleared with a reload of the game.
I do think I have a workaround for you guys though, if you coc into the basement and take the elevator up, the bug doesn't seem to occur in NJ's save. So it might be that loading from the exterior into GNN with something in the save file is a problem, but loading between interiors probably gives the game more resources to properly load the cell.
Can you guys test this idea out and let me know if it works for you? The command would be:
coc SS2C2HQBasement
If that works for all of you, I could make a quick and dirty patch for you that moves the fast travel point to the basement.