Ever since the upgrade to 3.3 I am unable to have php.ini in my folders.
I had this file to declare what the max file upload sizes where, but now if I have them I get this:
http://prntscr.com/1k05hm
If you have a dedicated server then you shouldn't need custom php.ini files in the htdocs/public_html directory as it its better controlled by the global php.ini.
Have you made any changes to php?
Such as phpsu phpsuexec? As I phpsu has global over rides to stop the use of custom php.ini files
