Yes you right, I tried fresh image and background in launch menu is black.
But this is more cosmetic problem, much bigger issue is delay before any emulator starts for about 3 seconds.
Can I shorten this delay and maybe add some command in /opt/retropie/supplementary/runcommand.sh to change this blue background color in black.
I have lots of customized settings and I dont want to start over with fresh image if possible.
Recently I sucessfully make upgrade from whezzy to jessie and update retropie from 3.0 to 3.6, without any other issues, except those I mentioned in my initial post.
If its possible to correct this, it would be almost perfect migration, because everything else works just fine.
Also can you specify what config listing you like to see?
I think that this problem is related with runcommand.sh, but I dont know how to change background colour in emulator launch menu and shorten appearance of this launch screen.