All Speakers Come in and out

Ok, first this is going to be long so bare with me I want to put everything we have done out there so people can give me more ideas. First we are redoing the system in our project car and we took everything out except for the HU. Well we got the box done put it in and tested the subs last night and they were slamming we shut everything down. Today we get home from work and we hook the subs back up and there is like very little bass and then BOOM bass kicks back in and then back out (amp does not go in to protect mode). Well we thought it may have been a voltage thing because last night when they were working the car was on. So, we hooked everything back up amps, cap, X-Over and line driver. I turn the car on and very little bass then BOOM it kicks back in then out. We check the amps and we are getting between 12.7 and 12.2. So, then I thought it may be the deck its a JVC LHX550. the reason I think that is because a couple of weeks ago when we took everything out I forgot to take out the main fuse and one day I smelt something and I looked in the trunk and the main which is 1/0 was sitting on one of my RCAs and melted the crap out of it, and with that said I don't believe its good for the deck to be getting nailed with 12Volts on the line out. Please any help would be great. We had a show to go on Sat and now we are dead in the water. And yes when working on mine or anybody elses the main fuse is being pulled before I even open the trunk. Also, I checked the subs coils to see if they were open and on all 4 coils I was getting 0ohms so, I know the subs or fine. We hooked them up and I checked ohmage again and coils were still closed and when you pushed on them I got readings to show the coils were opening and closing. Thanks Wade

I do not have another deck at the moment and I am going to replace the RCAs in a little bit I just woke up and about to feed my big ass and I am going back to the car. Thanks i will post later today and let you know what I figure out. Thanks