I have done some further research and have narrowed down this problem.
Other people see to have had this, but I can't see a solution yet.

MySQLi isn't working because it's not loading, because php.ini isn't
being read.

php.ini IS read if I use CGI, but not if I use ISAPI.

I have checked the obvious (it is NOT called php.ini.ini), have tried
it in various locations and restart IIS each time. PhpInfo reports
php.ini as being in c:\windows.

Any help greatly appreciated.