It turns out that when I was restarting logstash all of the processes weren't being terminated. My config files weren't the problem.
Here are the commands I ran to solve this:
ps -ef | grep logstash
sudo kill EACH_PID
sudo kill -9 PID_THAT_WASNT_KILLED_BEFORE
sudo /etc/init.d/logstash start
Thank you @magnusbaeck for all of your time and help!