Comment 5 for bug 1628707

This problem has been around for a long time now...

It's probably compiled-in, and comes from the region face setup. By default, the region face background is set to gtk_selection_bg_color, which must correspond to light grey.

It's possible to change this from the X interface in Options => Customize Emacs => Top-level Customization Group, and from there going to the following subgroups : Faces => Basic Faces. Scroll down to the region face, and choose the background of your choice. Then, go back up in the buffer, click Apply and save and you're done.

You could also choose another theme instead : Options => Customize Emacs => Custom Themes. Choose your theme and click Save Theme Settings.