I get abandon checkouts for the orders that were charged frommy client via 3rd party payment gateway

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Hi Shopify,


I need urgent help! Since last Friday I have been getting abandon checkouts continuously, yet my customers are being charged for those. Therefor every time i need to create a manual order to the abandon checkout and full fill that order. How do i figure out the root cause for this? Because from the Shopify administration accout i dont see anything wrong with configurations. 

I feel that shopify is not picking up the online payment order response message correctly therefor not creating an order, instead, its sending succesful transactions to the the abandon checkouts. Please help ASAP as this is causing a major inconviniance to my customers and they are wondering why they are not receiving a order confirmation after they pay.

Looking forward for a prompt response.