Amp is shutting down, Need help

So I had my stereo upgraded a few weeks ago. Its not a big system. I have a 10" JL audio sub, 4 kicker 5.25" in boat speakers and 4 Kicker 6x9 tower speakers. It was being powered by a 4 channel amp and mono channel amp for the sub. I had the head unit replaced with a Pioneer DEH9600 deck and the two amps replaced with a single NVX P900.5, 5 channel amp. I also had the kicker dual zone controller added. The sound is great but even mid volume level the amp will work for a few minutes max and shut down. If I turn it up higher then it shuts down. Using the gain control didn't cure the problem. Concerned it wasn't getting enough power from the batteries I put them on the charger and its still doing the same thing. I'm looking for any suggestions. The system was working fine before the upgrades. If I turn the stereo off and then back on the amp will start working again but will shut itself off. After about ten seconds of shutting itself off the sub will start to come back on and make a bit of a hollow thump. I'm confused. I really thought the batteries were the culprit but the charger showed the voltage at 12.8V. Any recommendations?

What is the RMS on the tower speakers? Is each channel running a single in boat and a single tower speaker in serial? Are you running the amp bridged?
Seems to me that's a lot of speakers running off a single amp. I would think that's a 2 amp minimum setup.
I guess we need more info.
Sounds to me like maybe you had someone set up the new system? Have you talked with them?

Thanks, its fixed now and was something stupid. Wingnuts on one of the batteries were loose and was arcing. Once they were tightened up all is well. Somehow that was making the amp shutdown. The amp does 100 watts per channel RMS and 300 RMS for the sub. 2 channels for the in boats, 2 channels for the tower and one channel for the Sub. Seems to do well.

That's a lot of speakers on a single amp. You're basically getting 50W per speaker at 14.4V (which isn't realistic). Expect to lose about 25% of that power due to lower voltage, so you're probably seeing shy of 40watts to each speaker with that amp. Even though it's working now, you'd probably still be better off adding another amp that allows you to dedicate a single amp to your tower speakers, and everything would sound even better.