Ok, the problem solved itself by entering Persephone. But still, that's a huge bug for a good portion of game time.

And on the subject of the Persephone area...

HOLY MOTHER OF CRAP!
Spoiler Alert, click show to read: 
You get to play a Little Sister! Gathering ADAM and vent-running and everything! And jeez, it's creepy since you now get to see the world through the eyes of a brainwashed girl. Everything is so pristine and perfect... white pillows on the floors, red curtains on the walls, the "angels" are beautiful women sleeping soundly instead of horrible Splicer corpses... and your vision occasionally comes back to normal for a few seconds, slowly letting you absorb the full mind of what's going on inside their heads.