Before I go ahead...I know there are MANY reasons why ranking can change.
But I have found that since upgrading to 5.5, it seems that many posts that enjoyed consistent very high positions for certain words have plummeted off the search pages.
I have noticed a common theme - Google is listing the category, but the individual post does not show at all.
Is this some sort of duplicate content issue - from what I can tell, I don't think any pages are in the supplemental index.
Not sure if this is a Sem Pro issue, but I have been noticing on my daily google alerts for "site:", one of my sites that is still on the last version gets its posts listed under regular sites with categories and tags, while the site that is on the latest version only gets its posts listed on "blog alerts" while categories and tags are listed under the site alerts.
George is correct. Category Excerpts should be off be default on upgrades. This behavior is changed for future upgraders. Users of 5.5+ will need to set to off.