Currently the official BOINC Manager does not have a systray icon under Linux. This is not Ubuntu's fault, Berkley itself simply does not provide such option. Years ago it had an -s option, for systray, but not anymore.
Yes, I also noticed the icon on Unity Launcher sometimes maximize itself. A bit annoying perhaps, but no big deal.
A workaround, if you don't want the window to pop (or the icon on Launcher), is to exit the manager, while leaving the tasks running in background:
Boinc Manager > File > Exit BOINC Manager (Ctrl+Q)
It will ask whether you want to also stop the tasks, and if you want to remember the decision. If you choose to leave the tasks running on background, they will show up if you run the Manager again.
Warning: if you choose to stop the tasks when you exit the Manager, you will have to manually start the Boinc service before the Manager works again. You can simply reboot your PC or type in either terminal or Alt+F2:
gksudo /etc/init.d/boinc-client start
Type in your password, and the Manager will work again.
If you set the Manager to remember the decision and you want to change it, you can do so by:
Boinc Manager > Tools > Options > "General" tab
And check "Enable Manager exit dialog"
This may mitigate any nuisances you may have with Boinc in Ubuntu.
Last but not least, if you really want a systray icon, and you're felling adventurous, you can try this unofficial, unsupported and perhaps outdated systray app. You may also need to whitelist the icon. Of course, try at your own risk.
