I have the exact same problem as reported here, only 7 years later (actually, two problems)
It only shows on AMD hardware (RX 560).
We have a doom3-based 2-stage deferred renderer.
It works more or less OK with a basic lighting. Now we want to add two textures to fragment shader: depth and stencil.
With GL_DEPTH24_STENCIL8 it works with halved FPS.
With GL_DEPTH32F_STENCIL8 FPS is back to normal but the stencil texture is corrupted.
It looks very much like driver bug but hopefully there must be a workaround for it.