I agree. Troubleshooting wise, I tend to lean towards disconnecting all the components one-by-one, and hopefully the noise goes away at some point, which would identify the issue. It could be amplifier related. It could be wiring related, or it could be a single source causing the issues. I've seen wiring done wrong so many times that it blows me away. Even wiring between a mixing board and a amplifier gets screwed up like crazy.
I did a job where the system had a balanced amplifier, but a unbalanced source. The client asked me to upgrade their audio system after I moved the system from their old location. Found out, when I reinstalled it, that it had been wired wrong for years. I fixed the wiring and the system played back audio at about ten times the volume it could before with perfect clarity. (that's what happens when you wire unbalanced stereo as balanced mono!)
At the end of the day, this really does require a specialist. As mentioned, those who did the installation/upgrade work when there was NO problem, should return to take a look at it since there is a problem. You can request that someone other than the installer come out to troubleshoot. My last company employed both installation techs, as well as a service specialist. The service tech requires far more training than a installation technician as they must know the ins and outs of troubleshooting.
For remote support, as has been mentioned, we would need a much better idea of what all is connected and how it all goes together.
I did a church setup and replaced their old analog board with a full digital DSP. It allowed them to plug in a analog board for major productions, but gave them one-touch usability for weekly congregations. I would say that most churches, unless they have a fairly well trained staff in AV, should have as simple as a system as possible.