Same flickering brightness problem for me.
It continues until Ubuntu finishes loading all startup programs - then it stops 
at some level.
I recently switched to Karmic Koala Alpha 6, problem was not in ealier (stable) 
releases.
I am also using MSI Wind U100.

Steps to reproduce:
1. switch Ubuntu 9.10 to Karmic Koala Alpha 6.
2. boot
3. screen with progress bar is shown correct (with no brightness abnormal 
behaviour)
4. at gdm prompt for user/password details - screen brightness starts flickering
5. flickering continues until all apps are loaded in Gnome.

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screen brightness flickers at login screen
https://bugs.launchpad.net/bugs/423873
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