Can not reproduce this. On a new Install the box is not visible only on a upgrade (when the forum is installed) then the box should be visible.
I've periodically been updating my site with the changesets of 2.0 and every time the upgrade bbcode checkbox has been there.
For last few weeks the "Upgrade BB" checkbox was hidden for both new and upgrade install. It is appearing now for upgrade install (I havent checked it for new install).
BTW how does YAF know whether it is new or upgrade install. Does it check app.config for password and database for specific tables?
Also should this checkbox be hidden for upgrade install, since it is giving error message (or atleast it was few weeks back as per earlier forum posts)