I can confirm this bug too.

It only happens with xinerama enabled.

When I open a gnome-terminal, focus on another window (does not need to
be a terminal), and click into the terminal to focus it again, it
immediately selects a whole line.

Happens with any visual effects setting.
xterm unaffected. 

This never happens without xinerama (not even on a dual monitor setup).

I have Ubuntu 10.4 x64 with the latest fglrx binaries from AMD.

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Desktop Bugs, which is a bug assignee.
https://bugs.launchpad.net/bugs/445084

Title:
  click-to-focus window is too sensitive

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