Thanks for the info and the screencast, it demonstrates perfectly the issue.
I am puzzled as I'm not experiencing the issue in a fully up-to-date 16.04 VM.
Could you please share the output of the following commands:
apt policy chromium-browser*
grep -n Exec /usr/share/applications/chromium-browser.desktop
I assume you're not seeing this with any other application?
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Chromium is Adding Unnecessary Additional Launchers
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