On my intel gpu (maybe others) when running atom there is lots of artifacts particularly around the windows although in many other places it will flicker with black squares as well, disabling "texture from pixmap" in the GL settings seems to fix this issue, although it doesn't seem to fix it for chrome which also shows similar behavior at times.
hmm just a note. egl/gles works on nvidia again. there are performance issues though vs glx. on nvidia only. on everything else perf is the same.
the artifacts you see i think are likely a synchronization issue at the driver level. hear me out. many gpus today divide the buffer into tiles or regions and render each on separately. they replay all render commands per tile. they may throw multiple tiles at different render units at the same time. it might be that the resulting buffer is not finished rendering to before e uses it as a source texture. there is now ay to know if it is finished or not yet. it shouldn't be swapped (and used) until the rendering is done OR the gpu should ensure it auto-fences the rendering with source use by another process.
this is my guess. it has something to do with this. a different kernel, driver (update) might help you. i have 2 atom systems and do not see your problems (in x or wayland). i am assuming your driver might have issues or issues specifically with your atom chip revision