It's hard to say without hearing it. That could be a a few things. Check for a blown speaker by playing some music at a decent volume and listening to each driver individually. Don't hurt yourself though, just put your ear to each driver. If it sounds funny, listen to it's partner on the good sounding speaker to compare.
If the sound is coming from a driver, it could be a loose part internally to the driver or something more complex happening inside the crossover circuit. If you can localize the sound to a specific driver, try pulling that driver and looking at it carefully. Look for anything stuck to it (like a screw to the magnet, etc) or something behind the cone (damping material, dust bunnies, whatever). If there is no obvious problem, try gently pushing in on the cone to check for a voice coil rub. The cone should glide or even bounce, but definitely not scratch.
If all the drivers work, it could be a loose piece inside the case. Diagnose by pulling the woofer and taking a look inside. You might have to pull everything off to get the best look. It's not uncommon for the internal bracing to come unglued and slap. Also check that everything is firmly attached to your crossovers by gently touching each piece on it and checking if it is loose. Make sure it's unplugged for that. This is a good time to check and replace fuses. If they are foggy or burst, replace them with proper replacements - fast acting fuses of the right rating. Also, if you have an ohmmeter, you can also check again that all drivers are working. Finally, make sure there isn't any loose junk in the bottom of the inside of the case that could be vibrating harmonically. If there's nothing loose inside, put all the damping material back in the case the way it came out, give it one last college try, and return it to the store if the noise is still there.
Hope to hear that everything works out for you.
