Orders that have been shipped take a very long time before they are confirmed in Amazon.
Amazon Limitations
There is a critical limitation on volume which is imposed by Amazon. In an entire 24 hour period you will never be able to confirm more than 735 orders per merchant! If you have trouble with this, Amazon or the FTC are the ones to contact about it (because Amazon only places this restriction on 3rd party fulfillment and not on Fulfillment By Amazon).
There is an important limitation on volume which is imposed by Amazon. Amazon only allows an average of 1 ship confirmation every 2 minutes.
This limit is imposed by Amazon. The order is held until the next time we can access Amazon. Different "feeds" in Amazon have different restoration quota - If we use up all 15 transactions, we get transactions back at a certain rate. For order confirmations we get 1 transaction back every 2 minutes. For orders pulling it is a little faster.
Extensiv Integration Manager can handle order volume spikes (with delays), but if the order volume is constantly exceeding the quota hour after hour, day after day - then it can be a big problem. This is Amazon's policy and not a shortcoming of Integration Manager.
The only available solution is to process Amazon orders first and confirm them ahead of other orders to get more time for the shipping confirmation process.
Amazon only poses this limitation on 3rd party fulfillment and not Fulfillment By Amazon.