I had the same issue and this seemed to work for me:
echo "apc.filters = wp-cache-config" >> /etc/php5/conf.d/apc.ini
echo "apc.include_once_override = 0" >> /etc/php5/conf.d/apc.ini
Hi there. Just curious if this feature request is planned to make it into production. Would love to see RRS support for W3 Total Cache.