I read somewhere awhile back that you can add
export PHPRC = "C:\Inetput\wwwroot\site1\conf;C:\Inetput\wwwroot\site2\conf;"
to your master php.ini file (typically located in C:\php) to allow it to recognize the local php.ini files in your various shared hosted sites.
All the local php.ini files would be placed in
C:\Inetput\wwwroot\site1\conf
and
C:\Inetput\wwwroot\site2\conf
I can't seem to find the site.