Thanks everyone for testing, the branch has been merged as of 4.0-1192.
@ Gundark: I wanted to test your issue again, but then noticed that recent nvidia drivers crash Dolphin's OpenGL backend. I'd like to look into it again at some other point when that issue is fixed, meanwhile can you verify that the issue indeed still happens with the 4.0-1192 builds from http://dolphin-emu.org/download ? There have been a few behavior changes since then, not specifically addressing your issue but maybe they did fix it anyway.
@ Gundark: I wanted to test your issue again, but then noticed that recent nvidia drivers crash Dolphin's OpenGL backend. I'd like to look into it again at some other point when that issue is fixed, meanwhile can you verify that the issue indeed still happens with the 4.0-1192 builds from http://dolphin-emu.org/download ? There have been a few behavior changes since then, not specifically addressing your issue but maybe they did fix it anyway.
