Jack,
Since you see the problem only when running a non-Ubuntu kernel, it
sounds like it is a problem with that kernel, rather than with xorg
itself. You really need to report this issue to the people you got the
broken kernel from.
** Changed in: xorg (Ubuntu)
Status: Confirmed => Won't Fix
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GL applications leave artifact lines on screen, application unusable
https://bugs.launchpad.net/bugs/255001
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