Please don't take this wrong, but often the shooter has a direct connection to POA/POI differences.
I've 'fixed' more situations where the "gun is shooting low" by fixing the shooter instead of the gun.
For example, the other day one of our new instructors was trying to help another person who was consistently shooting several inches low at close distances (7 - 10 yds). After watching them both struggle with the 'problem' a bit, which resulted in some frustration on the part of the shooter, I wandered over and got involved.
Listening to the "gun's shooting low" explanation, I took the gun and calmly discussed some of the shooting basics with the shooter, and then handed him back his gun ... which unknown to him now had an empty chamber.
I asked him to carefully fire an aimed round ... and watched the rather dramatic downward flinch as the hammer fell on an empty chamber. Well, that probably explains the 'shooting low'. He couldn't feel it when it occurred, because of the recoil, and the new instructor hadn't observed it, being focused on the point of impact at the target.
More importantly, now the shooter actually understood what was likely causing his problem. Instead of just 'being told' that he had a problem, he'd been able to experience for himself, feeling the downward flinch in the absence of recoil. Once he actually experienced and understood what was happening he was able to take steps to correct his 'problem', with some suggestions and further shooting drills. Of course, now he's got to make sure the 'fix' remains in place each and every time he presses the trigger ... same as the rest of us.
Ball & Dummy drills ... mixing dummy rounds with live ammunition ... can often help an instructor diagnose whether the shooter is unintentionally (and unknowingly) flinching, or having problems with his/her trigger stroke, etc., etc..
Personally, I prefer to mix in a Dummy round without the shooter being aware of it, so the shooter's expectation is that the gun is going to fire and recoil. I've often found that if the shooter 'expects' the Dummy round, then the shooter is focusing more on anticipating the Dummy round and less on his/her shooting. Temporarily 'training' to expect and handle the Dummy round in that specific drill, so to speak.
I've often wondered whether in some instances this developed a temporary 'false' skill correction on the part of the shooter, since some of them have only seemed to 'correct' their anticipatory flinch in their desire and expectation of 'passing' the corrective drills ... and returned to flinching once they knew all live ammunition was again being used.
This is best done in the presence of an instructor who can also observe whether other bad habits are being demonstrated (unknowingly) by the shooter. It can save frustration. It's also safer.
The trick is getting the shooter past the point where the shooter is just "expecting" the Dummy round in a training situation ... to where he/she is able to translate his/her recognition and understanding of 'anticipatory flinch' into being able to prevent it from occurring in regular live-fire training circumstances (where Dummy rounds aren't being used). Different folks may have a slightly different 'software/hardware' experience when they're being helped to resolve this sort of skill issue.
If it's actually a gun problem, then it's the sights.
It may also be the nature of the sight picture/alignment (POA used by someone who typically shoots 25 yd bulls-eye with a 6 o'clock hold, for example, and experiences 'low hits' when trying to use that sight picture at 7-10 yards).
Might also be the ammunition, upon occasion. As far as the bullet weight? The standard .40 S&W load around which the cartridge was developed used the 180gr bullet, and sometimes lighter bullets may impact a bit lower for some folks.
Of course, over the years I've also encountered the occasional situation where it's been caused by both the shooter's anticipatory flinch AND the sights ... and both have had to be corrected. That can be an interesting balancing act ...
Just my thoughts. Don't claim to have the answer. The internet can't replace an actual instructor. Nor can it diagnose and repair an actual gun problem.
If you call S&W they'll probably offer to send a repair tag so they can examine the gun itself, but then it might be understandably frustrating if they return the gun without having found any 'problem'.