You changed from CGI to PHP, did the URLs of your pages also change,
i.e. www.example.com/some_page.cgi to www.example.com/some_page.php or
did your site have "permanent" URLs that didn't depend on how they
were generated such as www.example.com/some_page/

If so, did you use 301 Permanent Redirects from the old URLs to the
new?

If the URLs changed but there were no 301's from the old to the new,
any PageRank associated with the previous URLs, as well as any links
to any of them, were essentially thrown away and until Google figured
out that the old pages were actually gone, Google would basically have
thought you had two copies of everything.  One set of pages with links
to them but errors when the pages were requested and another set of
pages with the same content but no links to them from other sites.

Is it possible this is what may have happened?

Craig