I can confirm this, it's been around since alpha1 or alpha2 at least.
Ctrl-L / refresh/ reset also works to fix it.

Compiz is turned off, so that's presumably not the cause.

It happens after every couple of commands, and happens every time I'm in
an xterm.

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xterm does not want to update window
https://bugs.launchpad.net/bugs/273196
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