SmallCaliberCentral

Sorry for the newbie type question but my searching wasn't finding what I am looking for.

My new Savage 12 FV has a long throat. I can't get very close to the lands with the SBK 39. Accuracy has been consistenly under an 1.25" but of 18 groups fired thus far, 12 have two touching with the third hole 0.5 -.75" away. I haven't kept good records, but it seems to be random which shot is the off shot. It could certainly be shooter error!

All rounds have been loaded to the same overall length.

Which variable should I be working with to lessen this tendency?

I have a Savage mod 12 as well. Instead of moving towards the lands, start moving back. That's what it took to bring my groups down to .375". Some fine tweaking and I believe I can get even tighter. I don't measure OAL. I measure from the ogive. Seems to be less variation that way.
Also, just neck size the cases, bumping back the shoulder just enough to chamber easily if necessary.
Oh, just a comment about powder. I started with H335 as that was what the Lyman manual said had the greatest potential for accuracy.
Well, it was pretty accurate but even with a moderate load, I was getting overpressure signs on a warm day. Switched to 8208 XBR and haven't had that problem and the accuracy is just as good.

Also check to see that your barrel and tang is floated. If not already glass bedded, I would recommend doing it, it could very well eliminate your flyer. I bed all my Savage builds and never have problems with flyers (as long as the handloads are put together with care). Measure your bullets from base to ogive, you'll be surprised at the wide variance in the lengths. With a Hornady L-N-L OAL gauge, you can measure from base of case to ogive AND know exactly how for from the rifling you are. With the Hornady gauge, book OALs are useless when you know the distance to the lands in YOUR barrel.