When migrating several sites from a VM GPL installation that was initially set up in late 2007 none of these sites could be restored using their original mod_php Server API causing some of these scripts to not function properly but more importantly no longer get cached by eAccelerator or other php caching scripts.(xcache).
When restoring the message appeared: "Checking restored PHP execution mode .. .. mode Apache mod_php cannot be used, switching to FCGId."
I was able to fix this for all the sites manually.
Finally in Virtualmin under 'Website Options' there are only two options for 'PHP script execution mode': CGI wrapper and FCGId and this has always been the case since the first install and when creating new sites. After the manual changes however neither of these options are now selected(blank radio buttons).