I had the same situation. In my case the problem was that I had two configuration files for memcache in /etc/php5/cli/conf.d/.
php -i | grep memcache.ini
In my case the result was:
/etc/php5/cli/conf.d/20-memcache.ini,
/etc/php5/cli/conf.d/memcache.ini
To get rid of the warning message I removed the line extension=memcache.so
from the memcache.ini file.