Has anyone else had this happen with a SSA Automated Shipping Template?

SSA was applied to our FBM Standard Shipping template, which was set at a 2-4 day delivery time window. Amazon estimated the 'promised delivery date' based on our shipping history incorrectly, the order has it with a 2-day estimated shipping window and the order was delivered in 3 days - within our standard shipping setting period but not when Amazon estimated it would get there. We use a preferred carrier but got an OTD warning in our account for a late shipment we had zero control over. I removed the SSA setting to avoid this happening going forward, but have concerns we'll get fewer FBM orders coming in. I also asked Amazon to remove the warning under the circumstances but they would not. Are others having this problem, or is Amazon doing a better job of estimating SSA delivery times? I'm afraid to turn SSA back on after this happened - anything else I can do?