I can start Transmission minimized. Here is the version i tested:
transmission:
Installiert:(keine)
Mögliche Pakete:1.06-0ubuntu4
Versions-Tabelle:
1.06-0ubuntu4 0
500 http://ports.ubuntu.com hardy/main Packages
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Transmission doesn't start minimized
https://bugs.launchpad.net/bugs/215681
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