I found out what was causing issues. When I wrote a pin HIGH, none of the other triggers would work on the MP3 Trigger. In the manual, it specifically states that you can set them HIGH at 3.3v or 5v and trigger others. I have posted on the MakerJam forums but haven't got a reply yet.
So now I am just using pinMode(pin,INPUT) to stop triggering a pin then setting it to OUTPUT to trigger it with a delay(20) in between those. Any less then 20 it doesn't trigger.