Flipped pixels like this would pretty much have to be a digital issue. There's just no way an analog failure in the flyback, yoke or CRT would produce clean pixels with the wrong value like this.
If the same logic board works in your other SE/30, then check the voltage levels, especially +5V. Maybe it's out of range and causing glitches on the logic board. On the analog board, the only component I could imagine causing this would be the inverter U1, but even that seems pretty unlikely.
The white pixels track objects on the screen, but don't appear in the middle of the grey pattern on the background. It suggests to me a problem on writing to the VRAM UC6 and UC7 (check the continuity on the address lines perhaps).
