Out of curiosity do you have the Origami plugin installed? If so, it's a feature of the plugin (which can be disabled). Here's snippet from the README.
As a bonus side effect, any inactive panes are dimmed slightly (or, for you with dark color schemes, greyed slightly) so that you can easily keep track of where you're working. If you'd rather keep all your panes bright and cheery, set fade_inactive_panes to false in your user settings. Additionally, you can adjust the grey scale of the inactive schemes using the fade_inactive_panes_grey_scale (default: 0.2).