I think I found a solution myself actually... In nglide_config.exe i set a resolution of 1440x1080 instead of 1920x1080. This is a 4:3 resolution so there is only the playing area available to the game. So no area for the flashing. I have previously created the 1440x1080 resolution in my nvidia control panel in order to be able to use native resolution for games that stretches in normal 1080 mode... It isn't usually necessary in nglide games. But this seems to be an exception.
I'm having the same issues with the screen flickering. Mine is flickering in the top and bottom of the screen. That's with a Radeon video card too.
I applied the settings you suggested and viola it is repaired just fine. Thank you KajQrd.