The php.ini path CB and Joomla output is just the response from php_ini_loaded_file() function call. So that's the INI file PHP is actually using. Your other ones are not being used for whatever reason. Only your host will be able to resolve that.
Regarding "Install from Web" does it also not work on your live site? It seams to intermittently fail for unknown reasons at this time. I've purged the cache on our end if you'd like to give it another try.
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As promised, an update following my request to our hosting provider.
They manually edited the php.ini file to increase the upload_max_filesize and I've been able to the updates using Upload Package.
CPanel seems to have been showing the wrong values (file?) for the Home Directory file (it's a MultiPHP environment) for our domain.
I'll try to Install from Web next time I update, but I still want to thank you both for all your efforts even though I fell back on the method with which I am most comfortable.