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.

-- 
Screen Doesn't Refresh Properly
https://bugs.launchpad.net/bugs/237727
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