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Summary: The problem is that the user www-data had in ufficient permissions to run amixer.  To fix this you need to first determine the user that php uses:

echo exec('whoami');

Then I gave that user passwordless privelages to run one script under my account (jake):

sudo visudo

And insert this line, filling in your info:

www-data    ALL=(your username here - in my case jake) NOPASSWD: /home/jake/scripts/mute.sh

Then I put the command that I wanted to run (amixer sset 'Mic',0 mute) in the mute.sh bash file. And I executed the script in PHP as shown below:

exec("sudo -u jake /home/jake/Scripts/./mute.sh");

Now amixer mutes every time!