I stumbled across this post with the very same issue of TeamViewer not starting minimized when set up for automatic launch during Ubuntu system startup.
The method described by @MJB on Jan 27 at 16:02 worked perfectly for me (I'm running Ubuntu 10.10 32bit, all updates installed up to this date, with teamviewer_linux_x32_v6.0.9224.deb).
I do not experience the glitches described by @misterben on Feb 14 at 18:50.
I installed GDevilspie via Ubuntu Software Center, ran it, created a new rule and set up GDevilspie to show the following code in the "Raw" tab:
( is ( application_name ) "Teamviewer" )
( is ( window_name ) "TeamViewer" )
( minimize )
( println "match" )
The devilspie daemon is set to start up automatically during system start and teamviewer is set to start automatically via System --> Preferences --> Startup Applications (click Add, command: teamviewer).
It would be great if the developers of TeamViewer would integrate a start minimized switch for linux though...
Thanks MJB! :)