So... I'll take a shot...
Correct me if I'm wrong - it SOUNDS LIKE you are measuring your cases after trimming, then again after firing. Is that correct?
Are you trimming then sizing, or sizing before trimming? If you're sizing AFTER trimming, then not all cases will be the same resultant length before firing.
To be honest, I'd really say that this is largely irrelevant. I'm a numbers guy if there ever was one, and I really can't say that I'd put any value in measuring my cases after firing, other than to confirm my chamber dimensions to know how far I need to bump the shoulder and prevent over-working or stretching at the shoulder. I suppose if you're bumping your shoulder too much, as the case obturates, it either has to draw the case neck shorter as it fills the shoulder, or it has to thin the wall at the shoulder.
It also sounds like you're measuring COAL, then chambering and NOT firing rounds, and experiencing either bullets getting pulled, or getting set back. Set back is pretty common in AR's, but also pretty simple to fix. I'd be surprised if they're getting pulled, since the 6.8 SPC mag length COAL really shouldn't let you get into the lands to pull the bullets at all. Bullet set-back is a big issue.
For factory chambers that don't have tight throats, I generally figure around 3-4 thou for neck tension. So bullet diameter plus twice the neck thickness, minus 3 or 4 thou.