I'm wondering if this could have something to do with the way you sterilize your equipment before you make the seedlinggraft?
Well, I think I work very clean, sterilizing blade with alcohol after EVERY cut. And if the problem were in sterility, the grafts just wouldn't take and start rotting, I think. And the 1st year's growth is good or very good (I usually regraft only on the second year).
But what I've made wrong all the time, I guess, is that I let shoots of rootstocks grow after the first winter. Initially, I remove them very thoroughly - but after the scion is growing well and is pretty big already, I do not pay much attention to the shoots. Yes, finally I do remove them indeed(and use for propagation) - but it's not uncommon that I let them grow up to, say, 10 cm long. Now, if you look at the last pictures closer, you see that necrosis appears above and only above the shoots of the rootstock. Principally, it could easily be that it's just the other way around and shoots emerge because of this necrosis - but I do not think so. This way or another, from today on, I'll not let the shoots of rootstock grow any more.
Would be interesting to make an experiment and graft something not very valuable to
Pereskiopsis or/and
Selenicereus. Say, (2x)120 grafts. And then (after every two month) to cut 10 of them into pieces. This way, the dynamics of developing necrosis could be observed during two years... But who has 120+ rootstocks for wasting this way? At least I don't!