Thanks for your detailed investigation.
I think the main problem is incorrect virtual size with panel.
When the second monitor is connected, then virtual size is taken from external 
monitor and X runs perfectly.

You said that after add checkpoints, the X have started correctly (some timing 
issue?).
Could you please check which exactly checkpoint is needed to run X correctly?

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[K8M800] mouse pointer corruptly displayed at the bottom of the X screen
https://bugs.launchpad.net/bugs/386740
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