Dude, don't quote me because I may be wrong, but it sounds like your subs are being underpowered. The MTX brand subs (especially the 12") require a lot of power, and when a sub isn't getting the power it needs it makes that "farting" noise. Most subs actually blow because they are underpowered as opposed to being over powered.

Try turning your gains up to see if it continues to make that noise. Also, how do your have them wired? If you have them wired normal (parellel) try bridging it to get more power to the subs (if your amp is stable at bridging). I don't know the specs of your amp. Your subs could be blown already because of the underpowering, but just turn up the gains or re-wire to check.

Another possibility is that you may have a hole in your box and the air escaping is making the sub to do that "farting" noise, but most likely your subs are being underpowered.