Finally returning to this. It's hard for us to test, if it's so time-consuming. You can send large files via http://letscrate.com/
if we should have a look.
But the Poisson equation is a good hint; if different methods are used I'm not sure what would happen... The normal approach is to use FFT2D also for electrodes, even if you set periodic boundary conditions in all directions.
We can perhaps agree that this doesn't really pose a serious problem, it's just one point and the rest looks absolutely fine - very fine, in fact; it's not easy to get the potential profile right with such a large vacuum gap, this is possible thanks to the double contour integration in ATK.
The segfaults are another story of course. Memory?