There is a constant collision sound in the base. I think it's above the server room, but I just started and can't access the vents. Is there any way to reset the physics, or fix this bug. It's very loud and very annoying.

All you need to do is buy a hook to climb in. And if for some reason you can't do it and haven't done so much, you can just start over. 

One of the physics settings stops the prop interact sounds, I don't remember which!