Since they are the same engine, I figured they would be running the same code base, just with different databases. However Meta is at svn revision 3813 while SO is at 3772, nearly 50 revisions behind. What gives?
In the Meta announcement blog entry, Jeff noted that there'd be code-level differences:
Those would require code changes rather than just database changes, since there aren't database switches you can throw (yet) to change the wording on the site or disable wiki across the board.
And SF is at 3773.
It's likely that there's no pressing need (no must-fix bugs or must-have feature) that's worth the downtime of an upgrade (or the effort of a minimal downtime upgrade).
And the way SVN works, they could be identical checkouts, and someone's doing development on a branch.