I had problem that htaccess not working. When I reinstalled PyroCMS into a new server I got this problem.
You might have same problem.
what I did to fix:
There is a Bug in apache while using a2enmod, it doesn’t make any
so I edited /etc/sites-enabled/000-default this
Options Indexes FollowSymLinks MultiViews
allow from all
Notice that you have to have AllowOverride All
then restard apach2
hope it will work