Just updating on the issue. I am in contact with a Quickbooks team member who is in contact with Quickbooks Engineers through an open investigation. It appears that everything is ok my side and on my banks side and that the issue is with Quickbooks not automatically pulling through the transactions. A bank refresh was done by the either the Quickbooks team member or the engineers and the missing transactions came through. The latest transactions since then are not coming through so the issue is still ongoing. I will update once I know more, hopefully this will be sorted shortly and I do not have the headache of importing CSV files manually.