JS_Harris - 9:08 am on Jul 26, 2013 (gmt 0)
It would make no sense for Google to lower your rankings based on version of Joomla. I suspect that the problems you encountered during the upgrade however may very well have caused some problems.
I managed to block google from indexing more by putting a robots.txt
A robots.txt file entry will not stop Google from indexing urls, it will only stop Google from crawling the pages. The result is that Google will index the urls with a message saying they could not crawl the pages.
If Google is indexing pages you do not have then you need to make sure that those urls do not exist on your site and that they return a 404 error code when visited.
It may take months or years for Google to stop crawling those urls and reporting them in GWT. I occasionally see urls reported as 404 errors in GWT that have not existed since 2007.