Ever since I started using Yosemite (and now in El Cap), my Time Machine drive icon has been the generic yellow instead of the appropriate green icon. Toggling External Disks off/on from Finder > Preferences > General restores the icon but, upon restarting, it reverts. I read
What happens when your Time Machine drive icon changes and that fix seems to work.
Apparently, this is a common issue, although it doesn't affect the actual performance of Time Machine.