My guess is that you are the victim of “autolysis”.
The best answer/description I’ve seen posted in this forum regarding this problem was provided by @Ember . This is a link to the thread for the full conversation: Another 54C gem... Beef cheeks - #31 by Ember
Below is a quote taken from that conversation…
Bacterial bloom is also given as the cause of loss of meat during a long cook. The meat when released from the bag has an ‘off’ smell. Once again, the cause of this is not bacterial. The bacteria is rendered inactive long before it can create enough of a bloom to ‘turn’ the meat. What is actually happening is loss of product due to autolysis. This is the same natural process we make use of when aging meat. Enzymes contained within the meat commence the breaking down the meat. This process starts when the animal is dead. It is slowed by refrigeration, but not halted. At ambient temperatures, even in a 100% sterile environment, meat will ‘go off.’ At the temperatures used for sous vide cooking the process is sped up. Cooking low temps and long times is a balancing act to get the temperature low enough to produce desired results while cooking fast enough to beat the natural process of autolysis.
Autolysis is also the reason why pasteurised food will not last indefinitely under refrigeration. Pasteurisation and refrigeration have rendered bacteria within the product dead or inactive but the product can still go off over time. Autolysis is the reason why.
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