I'm running a windows 7 machine and I've tried many things and I'm still getting the black flashes on my video. I've tried both the new launcher and the patch from the german website, both work to put the game in 640 by 480 resolution, but I can't get rid of the screen flashes. My lowest default resolution for my sreen was 800 by 600 pixels so I created a custion 640 by 480 but that didn't seem to help. Also couldn't create a 512 by 384 since the test was failing.
I am running all three executables in windows 98 compatibility mode and as administrator. Any advice you might have would be much appreciated. Thanks!

If you have an Nvidia graphics card, maybe you forgot to set the "Timing" to "manual" when creating the custom resolution. You have to do this the first and only after it put in the resolution values, 512 and 384 in this case.

I've been also getting flashes whenever some desktop application plays a pop-up notification. Such as Steam, Yahoo Messenger, antivirus/firewall software and whatnot.
You could maybe check this out, too.