I looked at the driver during the "problem sound", and there is not any excessive excursion going on. That's what made me stick my arm in the port and hold it down. I first thought maybe the driver was hitting against itself when we didn't notice and caused damage. I put my ear to the driver while playing a scene that caused the rattling sound, and then to the port. It's much more noticeable with my ear to the port. Plus being able to put pressure on the port, which eliminates the sound make me suspect the port has come loose inside the box.
The best solution I can come up with is taking the amp and driver out, and getting rid of the ports. We can than take a saturday and add a slot port in place of the original ports. I just have to run it through winisd and see what's possible to save the box. I really don't think it's the driver, and I'd imagine PE wouldn't give us much of a hard time on the warranty because we're only using a bash 300 with it, and we never crank it.
Edit: Yes the ports were secure, we put a piece of rounded wood on each port side, then liquid nailed the ports into the groove.