Hmm, actually, let me think about this. If the grommet is missing, it won't affect the PCV valve, since it's still controlling the amount of air going into the intake. However, This is a closed system, and there IS a hose coming off the valve cover that pulls air into the inlet ahead of the throttle body, but after the MAF. If the Grommet on the back of the intake was missing, it COULD allow extra air to enter the engine through the hose on the V/C, which would be un-metered air. I suppose this might contribute to a "not running right" situation, but I don't think on the scale of the pcv valve being disconnected from it's hose to the upper intake.
Anyway, when you get it replaced, let us know if it makes a difference.
Dennis