If your food materials, zone surface, and packaging materials are coming back with acceptable APC limits, but your finished product is showing high APC...There were no positives for indicator organisms (salmonella, ecoli, etc)? Time to check the production environment to see where these are coming from.
Have you looked at your production workers? Could they be introducing something via smock/uniforms, improperly washed/dried hands, unclean gloves? If the APC of the finished product is not usually this high, then you want to check that nothing has changed with the aforementioned items. Same hand soap, no change in potable water test results, same paper towels, same gloves, same laundry service for smocks/uniforms.