Shooter,
I agree with AlanPF that you need to reconfirm this with more testing, but I had a similar experience with necked-up brass...and VLD's. I'd be looking for factors that cause differential pressure. Question: Is the base of the boattail when loaded below or above the neck/shoulder junction? Are you shooting them jammed or jumped? Reason I asked, in my case it was with Lapua 243Win brass necked up to 260Rem. On that brass, and using 130VLD's, I consistently threw off two really nice separate groups in any five shot group, but rarely one nice tight group. Jamming the bullets helped some, but did not eliminate the problem. I finally stumbled on the cause- it was my case necks, specifically the neck/shoulder junction, caused by my (poor) neck turning technique.
I had not trimmed the brass immediately before I cleaned up the necks the first time, so I had slightly inconsistent lengths. When I put them through the turner, I had some that cut into the shoulder material as it should and some where the turning cut just touched the neck/shoulder junction. This caused a "mini" doughnut to form inside the neck after a few loadings. The base of the bullet contacted this area (sometimes)and I could "feel" it hit when I was seating bullets (sometimes)- just a slightly snug feel on the bottom of the seating stoke (this was how I found the problem - seating pressure by feel). That difference was enough, on some of the cases, to induce higher pressure and a different POI. After carefully F/L sizing the brass, trimming it, expanding it again and and re-turning the brass for consistency, the issue mostly disappeared . I still got occasional slight flyers, but they were bearing length related with the VLD's, not from the brass. I found I had to measure/sort by bearing length if I really wanted them to shoot tight. I ultimately switched to Lapua Scenars and quit measuring bearing lengths altogether - not enough difference to matter.
Point is, I'd look closely at my case necks on necked up brass if I were you. It can be the cause of alot of small, difficult to diagnose ills....If the base of the boattail falls above the neck/shoulder junction, I'd disregard most of this, but you may still want to sort by bearing surface length and shoot a few groups - on a loaded round a difference in bearing surface length = a difference in effective seating depth and we're all pretty anal about that, plus the effect of differential friction down the bore.....
Elkbane