Bioshock: there are two flavors of positional tracking. The default positional tracking that is theoretically possible with every G3D game and DirectVR positional tracking. If available DirectVR positional tracking is a bit better since it changes the position of the actual game camera, but if you encounter any issues with it, just disable it on the DirectVR page of the vorpX menu. The default G3D pos tracking will still be available in Bioshock.
What you could also try is re-running the scanner if that happens. In Unreal Engine 3 games the memory addresses for DirectVR can become invalid over time. Usually not within the same level, but maybe sometimes they still do, can’t rule that out entirely.
Black Mesa res: the resolution isn’t set by DirectVR in this game, hence resetting the profile doesn’t change it. You have to set it manually.