Strange issue - changes to all php.ini files do not apply

I'm having a weird problem with php.ini. The goal is to upload files up to 100MB (most are 8 - 25MB) via a PHP script. It works perfectly on shared host and on my local setup. It works perfectly on my linode ONLY if the pics are 2MB or less. Anything larger returns "empty file" which according to the script means it did not write to the upload file.

After editing my php.ini settings in all 3 locations (/etc/php5/apache2/php.ini, /etc/php5/cli/php.ini, and /etc/php5/cgi/php.ini) in terminal with nano, changing postmaxsize and uploadmaxfilesize so that larger files can be uploaded. Everything looks good. I restart apache, reboot the linode, and even shut the linode down and boot back up. When I check info, the settings are default - not the updated settings. I check the file again by opening them in nano and by checking the info.php file, and the settings are correctly saved as I had them when I open in Nano, but the info file says they are default.

What could possibly prevent the info file and the system from reading my updated php.ini files?

Would really appreciate any help.