I've noticed something similar:
I recently completed a change from table-based layouts to div layouts on 5 sites. The sites still look exactly the same as before - it was purely a markup change invisible to the user.
All of the sites have lost places in the SERPS - not too many though (-2 places).
On another site, I removed a site-wide link to the Spanish version of the site. The immediate effect was that the site disappeared completely from the results, followed by a recovery to roughly 20 positions below its previous position.