I need to turn off safe mode and change the upload limit.
I've changed the .ini file in the server root and in the virtual site.
I have run phpinfo and looked in every ini file listed and they all show safe mode off or don't refer to it.
The list shows safe mode off under master value, but on under local.

Can anyone tell me where to look for thr file that's setting it on?

Any help is greatly appreciated.

Are you running any control panels? phpinfo should list the config files in the section labeled "Configuration File (php.ini) Path" and "additional .ini files parsed".