After digging down for several hours we have discovered a problem regarding the Virtualmin option to have a personalized php.ini file for a Sub-server:
We are pretty sure now that Virtualmin is doing something wrong and we have had to modify the global php.ini file to change the upload_max_filesize parameter.
The problem raised when we tried to set that option to increase the size of uploaded files. We are using Mantis Bug Tracker and after mounting it and changing the local php.ini, it was clear the option was set correctly and moreover the php_info function reported everything correctly.
Just after changing global php.ini, we got everything right and the desired value was correctly retrieved.
The value is read using the config_get function.