Since installing a GTX 1080, the Afterburner/RTSS overlay only works sometimes. I did reinstall Afterburner/RTSS latest version and started from scratch. I can't seem to find the pattern or why it works sometimes and not others. This happens in any DirectX version and Open GL programs.
Seems that by default support for 64 bit applications is not enabled. Once I checked this in RTSS options, it started working again.