That was the wrong save file. I have uploaded the correct save file on dropbox and put the link in the comments of the file you linked to.
The controls are gone for me too. That's weird. Have you tried loading an older save where they are there and progressing to that point? Maybe check back at each quest stage to see if there's a point when they disappear.
Edit: I just loaded up your older savegame and rushed through to roughly the same point as the later one (Envirosuit obtained, Alpha and Delta enabled, Deck 7 lift secured, about to enter Beta), and the controls were still there. Maybe one of the saves from inbetween still has them.