The bug came back after I imported bookmarks from Safari, even on the Beta channel.
To fix it, delete the Bookmarks file located in:
/~yourusername/Library/Application Support/Google/Chrome/Default/
Chrome automatically creates a backup copy named Bookmarks.bak
Once you delete the Bookmarks file, next time you open Chrome, it will load your bookmarks from the backup copy and there will be no more "poof" animation on startup.