Hi everybody!
I just subscribed this forum because of the same issue on my iMac with El Capitan.
For sure it's not a "major issue" since the most important thing is that backups work properly, but (for me) it's very annoying.
I installed El Capitan as an upgrade of Yosemite and I think this is the problem.
As far as I remember this issue occurred each time I upgraded the OS to the new one (from ML to Mavericks, from Mavericks to Yosemite and now to El Capitan).
So yesterday I made this experiment: I took my wife's macbook pro - officially my test environment
- and I installed El Capitan from scratch; after that I took a USB external hard drive and I set it as the TM volume and ... the green TM icon started working again !
The only one "issue" (but it was the same with Yosemite) is that when I restart the Mac the TM icon is shown in orange, but as soon as a backup completes it switches automatically to the green one.
Let's say ... better than nothing ...
In my opinion, in order to avoid "previous OS garbage", the best thing would be to install major releases by formatting the Mac but ... I know ... it's very bothering.
Ciao !