The problem is I'm using Unity, the theme is Ubuntu Mono Dark, and I'm using non overlay scrollbars so I'm having a hard time actually seeing the scrollbar.
This bug has been plaguing me since at least 2011 and it doesn't look like anybody has looked at this. See here for an actual bug report: https://bugs.launchpad.net/ubuntu/+source/ubuntu-themes/+bug/721786
I solved the non existent scrollbar in Google Chrome by installing the extension "Clearlook Scrollbar Theme". Since Google Chrome is my go to browser this solves the problem for the web. I managed to patch things up with Gnome Terminal and Gedit by editing some system files but I don't really count that as solving the problem since these fixes will get wiped out by updates.
For my other gnome apps I used the advice given here to install the addon gnome-color-chooser. I also edited the file "/usr/share/themes/Ambiance/gtk-3.0/gtk-widgets.css" around line 1500, but I don't really think this solves the problem.
