This is very annoying, and is affecting the top and bottom panels. I had the problem with Eoan too, but I noticed it only appeared if I have a tty session opened as the same user when starting Flashback. Now that I've upgraded to Focal it can't get rid of it, even if Flashback is the first session opened as that user.
I tried explicitly setting the background and text color (Alt-Right click on the panel), but I didn't manage to get back to what is supposed to be the default anyway. I simply would like it to behave like it's configured to. Any advice ?
EDIT : To make things clearer, I use the default theme. I tried with the Intel and the Nvidia GPUs (I have an Optimus laptop), same problem. And here's a screenshot :
Notice the white border of Windows too. It wasn't like that before...
2ND EDIT : It turns out my "problem" is not really one, the theme has changed in 20.04. So the problem would rather be "How to set the theme of Gnome Flashback to the previous default one ?"
So, for people like me wondering why the theme changed in their Gnome Flashback session since Focal, and how to get back to the previous default one, it's not a bug, the default GTK theme changed from Ambiance to Yaru, and the icon theme changed from ubuntu-mono-dark to ubuntu-mono-light.
HOW TO GET BACK TO THE PREVIOUS (AS OF 19.10) DEFAULT THEME :
apt install light-themes
Then, as the user wanting to change the theme :
gsettings set org.gnome.desktop.interface gtk-theme Ambiance
gsettings set org.gnome.desktop.interface icon-theme ubuntu-mono-dark
And voilà, back to the previous theme !
Thanks to @muktupavels for pointing me in the right direction.