This problem has been around for years, and ultimately linked to the fact that today's focusing screens ( which the camera meters from) are not linear relative to the incident light, and that the light incident to the focusing screen that the meters are reacting to has a huge dependence on the lens aperture.
Lenses with aperture contacts work fine in open aperture metering because the camera is told/programmed for their aperture, but move off open aperture metering (green button on non A lenses for example) and the metering is not accurate,
See the post linked here,
The graph began development in2007 (that's right 10 years ago)
Strange exposure problem but only w/teleconvertor - PentaxForums.com