Same deal here. With the graphics update I tried out the directx 11 setting since I've got a GTX570, there was flickering and constant crashes to black screens or desktop due to the graphics drivers failing. I switched it back to directx 9 and the nebula flickering has remained since. The game looked fine before the update and is an unsightly mess after. Nice upgrade Cryptic.
So I get a answer from Cryptic for my bug report. They write I should try starting the game on safe mode and try it with the standard graphics. If there is no problem I should raise the graphic step by step to see where the problem is. So I do what they say start the game on "safe mode" and yeah it worked. I can play DX9 and DX11 now without any bugs in the graphics. no flickering no missing textures. Only thing thats funny is I play on the same settings as in normal mode so I dont get what the problem is but as long there is no Problems in safe mode it works for me. Perhaps this can help some off you too.