Comment 9 for bug 237727

No, I've never seen this before in conky. Right now I've my suspicions on the intel driver (this is why I asked you to try the vesa one), but this is just a guts feeling. To force the use of the vesa driver, try to add the following to your xorg.conf file:

Section "Device"
        Driver "vesa"
EndSection

I don't know if that is enough since xorg autodetection messes things up a lot.
Another possibility is to exclude the window manager, for that try setting own_window to no and experiment with the other own_window settings.
Conky is pretty much a self-standing application, it talks directly to the X server through standard calls and uses only a couple of extensions (notably, xdamage and xdbe).

The problem seems to be a refresh problem, so it may be worth looking into the dbe part of the intel driver.