I deactivated the desktop effects, and rebooted the computer. I tried twice and 
had no applet issue. I reactivated the desktop effects and rebooted and the 
applet panel now doesn't show the login applet but shows the "IM/Ubuntu" one 
applet twice.
The bug seems to be indeed related to desktop effects.

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[i945gm] Duplicated and missing applets in the applet panel on startup
https://bugs.launchpad.net/bugs/584898
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