Thank you for your reply!
The reason for this problem is that we don't really have product lines. We have a meat cutting room where the carcasses come in. There are several people working in the room cutting the meat and each one is working on a different part of the carcass. Each person then puts their product on the same conveyor belt which takes it to the packing room. There we have people putting the different products in different vacuum bags or in some cases, large laminated carton boxes. The products in the vacuum bags then go to the vacuum machine but after that they go on the same conveyor belt that takes every product past the scales, through the metal detector and then into the cold storage room.
We have tried programming the metal detector with various products, but it doesn't work because the products vary so much.
Last year we got a guy from a company here in Iceland which specialises in validating and verifying metal detectors. He set up a few programs and taught us as well how to program the machine. But he basically said that this would never work, because the products vary so much in size and type. The weeks after I took various products, set up programs in the metal detector and ran them through. Then, when I added the test pieces, the machine did not detect any of them (I had F, NF and S/S). The largest piece is a 8.0 mm S/S, and maybe it would have worked with much larger test pieces but how would you defend having anything bigger than that since it is the smaller pieces you want to find in your product
I also tried programming the machine based on only one type of product and used marinated slices for that. That worked well and the machine detected when I added the test pieces. But....different kinds of marinade gave different results... 
Based on what I have read, and the comments here as well, I guess we will have to wait with the audit until we have put up another system for this...and I'm guessing x-ray would suit our company best
Ultimately the metal detector process isn't working. As Charles said above there may be some issues with set up as well but as you rightly point out, different marinades can have different ingredients in them with varying molecular charges so it will give a different product signal.
So for me, the problem is you're trying to run all these different products through the same metal detector without changing the settings. It is that which is meaning you cannot get consistent metal detection. You are trying to get a consistent result knowingly introducing a massive variable. In my view, I'd change your process so you can metal detect all products (or at least some) on their own setting. This may mean another metal detector or it might be something as simple as collating a quantity of finished product, e.g. 50 packs, setting up the metal detector and running them through as a batch?
As an auditor I would be highly suspicious of anyone undertaking a cutting operation without metal detection, at least on a manufacturing (rather than kitchen) scale. To try and "risk assess it away" also signals the wrong mindset to me. It's suggesting someone who wants an easy solution rather than the right solution. It's not the best impression to give someone coming in to look at your food safety systems.
Imagine if you will, a situation where you have a piece of metal that has made it to a consumer. It causes laceration requiring significant surgery. You are appearing in court.
Barrister "So Margerteva, you decided to stop metal detecting. Why was that?"
Defence witness "We kept getting metal detection failures and false positives."
Barrister "Why was that?"
Defence witness "We were checking multiple products at once."
Barrister "So it would have prevented my client being injured by your products had you got a second metal detector?"
Defence witness "Well..."
Barrister "Is that possible?"
Defence witness "It's possible."
Barrister "So I put it to you that you willfully made a decision not to metal detect your product because it was easier and cheaper, is that correct?"
Defence witness "I wouldn't say that?"
Barrister "So what would you say? I am to believe that metal detection is the industry norm?"
Defence witness "Yes that's correct."
Hmm.... I wouldn't like to be on the receiving end of REALLY having to defend that decision.