Can confirm the bug in Stretch. glxgears reports 45fps because it is using llvmpipe instead of VC4.
When enabling the GL driver via raspi-config, raspi-config should remove/disable /usr/share/X11/xorg.xonf.d/99-fbturbo.conf (e.g. rename it to disable it), but it does not, which results in Xorg not using the GL driver. A manual workaround is renaming this file manually (don't forget to rename it back when disabling the GL driver or you'll get no video!).
So this is IMO at least a bug in raspi-config.
Why jessie gives 180fps in glxgears even when using llvmpipe, I have no idea. llvmpipe is software rendered, it's not VC4 which is hardware rendered.
Can confirm the bug in Stretch. glxgears reports 45fps because it is using llvmpipe instead of VC4. X11/xorg. xonf.d/ 99-fbturbo. conf (e.g. rename it to disable it), but it does not, which results in Xorg not using the GL driver. A manual workaround is renaming this file manually (don't forget to rename it back when disabling the GL driver or you'll get no video!).
When enabling the GL driver via raspi-config, raspi-config should remove/disable /usr/share/
So this is IMO at least a bug in raspi-config.
Why jessie gives 180fps in glxgears even when using llvmpipe, I have no idea. llvmpipe is software rendered, it's not VC4 which is hardware rendered.