Greg, About the only way for anyone to consistently miss low birds from station one on a skeet field is to cross fire. The bird is for all intents right on top of you and as big as the moon, but pick it up with the wrong eye and you'll miss every time. This assumes a right handed shooter. As people age and /or get tired or suffer from eye strain [e.g., too many hours looking into the CRT of the 'puter] and stress some can have the normally 'off' eye just take over. That is one possibility.
Real long stocks are a hindrance, and it certainly could be or become an issue. You didn't mention how you were addressing the bird .. pre-mount, just off the shoulder and out of the pocket, under the arm, low gun?
The suggestion to go to theplate and pattern is a good one. For one thing it will eliminate or prove that regulation &/or POI is a contributing factor and if it was not then your confidence can move up accordingly. If it is then it should be addressed so that it is not.
Full chokes aside, Skeet is not a forgiving game. Rather, it has perhaps the lowest tolerance for doing anything wrong of any of the normally shot clay target games. You will see where some of the top skeet shooters have spoken of slumps and every time they 'go back to the basics' to get past it. Usually that is inclusive of a coach that knows what they are doing and some quality soul searching and thot on the part of the shooter to get back in the groove and bring their game back. Do anything at all wrong on a skeet field , even with a skeet choke and skeet ammunition and you just missed the target! It is a game of precision and one of repetition and exactitude.
I am aware that I have not diagnosed your experience's cause, but perhaps something said here will help you to do so. All of us has had off days and anyone who has tried to or that has become truely proficient at skeet has had to practice the basics and learn to not make mistakes, and that is irrespective of the 'method' being used. It applies just as easily to swing through as it does to sustained lead or push ahead or spot shooting .. every one of them reqiures precision. At 21 yards there is simply is no room for error.