I had the same problem with the first one I bought. I sent S&W an e-mail asking them if it was considered acceptable for me to put 18 clicks on the front sight to bring it up to only near the bullseye. They told me to send it in and sent me a shipping label. I got it back pretty quickly, I think it was less than two weeks, but they didn't do anything to fix it. Even though I included a detailed note and a copy of the target showing how low it shot with mechanical zero, they sent it back with a note stating that parts and springs were replaced to latest spec. Nothing was mentioned about it shooting low, and it still took more clicks than I could get my tool down deep enough to achieve in order to zero. And it wasn't the sights either. I put a Primary Arms red dot on it, and it took something like 26 clicks up to zero. I put the same optic on a SIG522 and I had to take about 20 of those clicks out to zero the SIG.
I sold that one but the two I have had since then have zeroed with two to four clicks on the front, as they should.