I did a test with my ET4000 ISA card and all are fine at 1024x768 /256 Colors. I not know what are the problem with your setup. I test with my Atari Mega ST4. The Mega ST has 4,7k pullups at the address lines. The Atari 260/520ST has 10k pullups, maybe that is the problem !?!
For the PAK68/3 you can change the Pullups for the address lines to 2,2k and the data lines to 4,7k.